ClinVar Miner

Submissions for variant NM_022662.4(ANAPC1):c.3100G>A (p.Val1034Met)

gnomAD frequency: 0.00192  dbSNP: rs548028803
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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 RCV000973228 SCV001120969 likely benign not provided 2018-07-04 criteria provided, single submitter clinical testing
Ambry Genetics RCV004029970 SCV004053646 uncertain significance not specified 2023-09-13 criteria provided, single submitter clinical testing The c.3100G>A (p.V1034M) alteration is located in exon 26 (coding exon 25) of the ANAPC1 gene. This alteration results from a G to A substitution at nucleotide position 3100, causing the valine (V) at amino acid position 1034 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Breakthrough Genomics, Breakthrough Genomics RCV000973228 SCV005262691 likely benign not provided criteria provided, single submitter not provided
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355438 SCV001550324 uncertain significance Rothmund-Thomson syndrome type 1 no assertion criteria provided clinical testing The ANAPC1 p.V1034M variant was not identified in the literature but was identified in dbSNP (ID: rs548028803) and ClinVar (classified as likely benign by Invitae). The variant was identified in control databases in 240 of 147822 chromosomes (1 homozygous) at a frequency of 0.001624, and was observed at the highest frequency in the European (non-Finnish) population in 165 of 59988 chromosomes (freq: 0.002751) (Genome Aggregation Database March 6, 2019, v2.1.1). The p.V1034 residue is conserved in mammals and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) 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 (Splice AI exome) 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.

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