chrX-154428794-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001183.6(ATP6AP1):c.102G>T(p.Ala34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000993 in 1,007,473 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001183.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6AP1 | NM_001183.6 | c.102G>T | p.Ala34= | synonymous_variant | 1/10 | ENST00000369762.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6AP1 | ENST00000369762.7 | c.102G>T | p.Ala34= | synonymous_variant | 1/10 | 1 | NM_001183.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 25
GnomAD3 exomes AF: 0.0000177 AC: 1AN: 56386Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 14194
GnomAD4 exome AF: 9.93e-7 AC: 1AN: 1007473Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 323685
GnomAD4 genome ? Cov.: 25
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at