rs199914263
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001692.4(ATP6V1B1):c.591C>T(p.Ala197Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,607,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001692.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP6V1B1 | ENST00000234396.10 | c.591C>T | p.Ala197Ala | synonymous_variant | Exon 7 of 14 | 1 | NM_001692.4 | ENSP00000234396.4 | ||
ENSG00000258881 | ENST00000606025.5 | c.476-18493G>A | intron_variant | Intron 5 of 5 | 5 | ENSP00000475641.1 |
Frequencies
GnomAD3 genomes AF: 0.000190 AC: 29AN: 152242Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000129 AC: 31AN: 239914Hom.: 0 AF XY: 0.000100 AC XY: 13AN XY: 129572
GnomAD4 exome AF: 0.000144 AC: 209AN: 1455146Hom.: 0 Cov.: 31 AF XY: 0.000130 AC XY: 94AN XY: 723168
GnomAD4 genome AF: 0.000190 AC: 29AN: 152358Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:2
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Renal tubular acidosis with progressive nerve deafness Benign:2
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not specified Benign:1
Ala197Ala in Exon 07 of ATP6V1B1: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wit hin the splice consensus sequence, and has been identified in 1/7018 European Am erican chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS). -
ATP6V1B1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at