Submissions for variant NM_001289808.2(CRYAB):c.325-2A>G

gnomAD frequency: 0.00002  dbSNP: rs202024436

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV000655022	SCV000776942	uncertain significance	Dilated cardiomyopathy 1II	2024-01-08	criteria provided, single submitter	clinical testing	This sequence change affects an acceptor splice site in intron 3 of the CRYAB gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. This variant is present in population databases (rs202024436, gnomAD 0.006%). Disruption of this splice site has been observed in individual(s) with clinical features of CRYAB-related conditions (PMID: 33906374). ClinVar contains an entry for this variant (Variation ID: 44235). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx	RCV001753446	SCV001994914	uncertain significance	not provided	2020-11-27	criteria provided, single submitter	clinical testing	Reported in one case of sudden infant death syndrome (Tester et al., 2018); Canonical splice site variant with an unclear effect on protein function; This variant is associated with the following publications: (PMID: 29544605)
AiLife Diagnostics, AiLife Diagnostics	RCV001753446	SCV002501408	uncertain significance	not provided	2021-05-28	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002444476	SCV002612431	uncertain significance	Cardiovascular phenotype	2022-09-13	criteria provided, single submitter	clinical testing	The c.325-2A>G intronic variant results from an A to G substitution two nucleotides upstream from coding exon 3 in the CRYAB gene. This variant has been detected in a victim of sudden infant death and in an individual with hypertrophic cardiomyopathy (Tester DJ et al. J Am Coll Cardiol, 2018 03;71:1217-1227; Ware SM et al. J Am Heart Assoc, 2021 05;10:e017731). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and may result in the creation or strengthening of a novel splice acceptor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. However, this alteration occurs at the 3' terminus of the CRYAB gene and is not expected to trigger nonsense-mediated mRNA decay. The exact functional effect of this alteration is unknown. In addition, loss of function of CRYAB has not been established as a mechanism of disease. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV002468991	SCV002766182	uncertain significance	not specified	2022-11-11	criteria provided, single submitter	clinical testing	Variant summary: CRYAB c.325-2A>G is located in a canonical splice-site of the last intron and is predicted to affect mRNA splicing possibly resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. While the variant is predicted to impact splicing, it is not expected to undergo nonsense mediated decay, therefore the impact of this variant on protein function is unclear. The variant allele was found at a frequency of 3.6e-05 in 250272 control chromosomes. c.325-2A>G has been reported in the literature in individuals affected with Cardiomyopathy related phenotypes (Tester_2018 and Ware_2021) without strong evidence for causality. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Three submitters classified as VUS while one classified as likely pathogenic. Based on the evidence outlined above, the variant was classified as VUS.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000037214	SCV000060871	likely pathogenic	Cardiomyopathy	2012-02-13	flagged submission	clinical testing	The 325-2A>G variant (CRYAB) has not been reported in the literature and has not been previously detected by our laboratory. This variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the highly conse rved splice consensus sequence. In summary, this variant is likely to be pathoge nic.