17-75040142-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006356.3(ATP5PD):c.241G>A(p.Val81Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_006356.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP5PD | NM_006356.3 | c.241G>A | p.Val81Met | missense_variant | Exon 4 of 6 | ENST00000301587.9 | NP_006347.1 | |
ATP5PD | NM_001003785.2 | c.220-871G>A | intron_variant | Intron 3 of 4 | NP_001003785.1 | |||
KCTD2 | NR_110835.2 | n.365+4785C>T | intron_variant | Intron 3 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151830Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251450Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135898
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1459778Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726216
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151830Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74158
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.241G>A (p.V81M) alteration is located in exon 4 (coding exon 3) of the ATP5H gene. This alteration results from a G to A substitution at nucleotide position 241, causing the valine (V) at amino acid position 81 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at