ClinVar Miner

Submissions for variant NM_000092.5(COL4A4):c.3018A>T (p.Arg1006Ser)

dbSNP: rs531161419
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000900474 SCV001044794 benign not provided 2024-01-29 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002502655 SCV002813777 likely benign Autosomal recessive Alport syndrome; Benign familial hematuria 2021-07-19 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000900474 SCV001551444 uncertain significance not provided no assertion criteria provided clinical testing The COL4A4 p.Arg1006Ser variant was not identified in the literature nor was it identified in ClinVar. The variant was identified in dbSNP (ID: rs531161419) and in control databases in 81 of 249572 chromosomes (1 homozygous) at a frequency of 0.0003246 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 80 of 30602 chromosomes (freq: 0.002614) and Other in 1 of 6064 chromosomes (freq: 0.000165), but was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), or European (non-Finnish) populations. The p.Arg1006 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of 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 the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.
Natera, Inc. RCV001830963 SCV002078879 likely benign Alport syndrome 2020-03-05 no assertion criteria provided clinical testing

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