ClinVar Miner

Submissions for variant NM_004385.5(VCAN):c.2618T>G (p.Ile873Arg)

gnomAD frequency: 0.00006  dbSNP: rs150395515
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000943417 SCV001089363 likely benign not provided 2024-01-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV002545962 SCV003724556 uncertain significance Inborn genetic diseases 2021-07-14 criteria provided, single submitter clinical testing The c.2618T>G (p.I873R) alteration is located in exon 7 (coding exon 6) of the VCAN gene. This alteration results from a T to G substitution at nucleotide position 2618, causing the isoleucine (I) at amino acid position 873 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001356175 SCV001551266 benign not specified no assertion criteria provided clinical testing The VCAN p.Ile873Arg variant was not identified in the literature but was identified in dbSNP (ID: rs150395515) and ClinVar (classified as likely benign by Invitae). The variant was identified in control databases in 36 of 281972 chromosomes at a frequency of 0.0001277 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Ashkenazi Jewish in 31 of 10352 chromosomes (freq: 0.002995), Other in 1 of 7194 chromosomes (freq: 0.000139) and European (non-Finnish) in 4 of 128436 chromosomes (freq: 0.000031), but was not observed in the African, Latino, East Asian, European (Finnish), or South Asian populations. This frequency is greater than expected for autosomal dominant VCAN-Related Vitreoretinopathy (Kloeckener-Gruissem_2016_PMID:20301747). The p.Ile873 residue is not conserved in mammals and four out of five 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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