15-25679435-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_024490.4(ATP10A):c.4406G>A(p.Arg1469His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1469G) has been classified as Uncertain significance.
Frequency
Consequence
NM_024490.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP10A | NM_024490.4 | c.4406G>A | p.Arg1469His | missense_variant | 21/21 | ENST00000555815.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP10A | ENST00000555815.7 | c.4406G>A | p.Arg1469His | missense_variant | 21/21 | 5 | NM_024490.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000509 AC: 128AN: 251336Hom.: 0 AF XY: 0.000464 AC XY: 63AN XY: 135852
GnomAD4 exome AF: 0.000181 AC: 264AN: 1461682Hom.: 0 Cov.: 32 AF XY: 0.000157 AC XY: 114AN XY: 727108
GnomAD4 genome AF: 0.000217 AC: 33AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at