3-113781044-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001690.4(ATP6V1A):c.83-6C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000277 in 1,445,622 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001690.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP6V1A | NM_001690.4 | c.83-6C>A | splice_region_variant, intron_variant | Intron 2 of 14 | ENST00000273398.8 | NP_001681.2 | ||
ATP6V1A | XM_047448305.1 | c.83-6C>A | splice_region_variant, intron_variant | Intron 2 of 14 | XP_047304261.1 | |||
ATP6V1A | XM_047448306.1 | c.83-6C>A | splice_region_variant, intron_variant | Intron 3 of 15 | XP_047304262.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP6V1A | ENST00000273398.8 | c.83-6C>A | splice_region_variant, intron_variant | Intron 2 of 14 | 1 | NM_001690.4 | ENSP00000273398.3 | |||
ATP6V1A | ENST00000703904.2 | c.83-6C>A | splice_region_variant, intron_variant | Intron 3 of 15 | ENSP00000515542.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000169 AC: 4AN: 236216Hom.: 0 AF XY: 0.00000781 AC XY: 1AN XY: 127964
GnomAD4 exome AF: 0.00000277 AC: 4AN: 1445622Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 719202
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at