ClinVar Miner

Submissions for variant NM_001166108.2(PALLD):c.1965-12565G>A

gnomAD frequency: 0.00004  dbSNP: rs368350042
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000123175 SCV000166480 benign Pancreatic adenocarcinoma 2025-01-11 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV003315815 SCV004016537 benign Pancreatic cancer, susceptibility to, 1 2023-07-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV001356302 SCV005463855 likely benign not specified 2024-07-29 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001356302 SCV001551431 benign not specified no assertion criteria provided clinical testing The PALLD p.Val156Ile variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs368350042) and ClinVar (classified as benign by Invitae). The variant was identified in control databases in 684 of 145410 chromosomes (13 homozygous) at a frequency of 0.004704 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 664 of 20284 chromosomes (freq: 0.03274), Other in 15 of 4572 chromosomes (freq: 0.003281), Latino in 3 of 23164 chromosomes (freq: 0.00013), African in 1 of 12862 chromosomes (freq: 0.000078) and European (non-Finnish) in 1 of 57790 chromosomes (freq: 0.000017), but was not observed in the Ashkenazi Jewish, East Asian, or European (Finnish) populations. The p.Val156 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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