13-24688392-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001676.7(ATP12A):c.302C>T(p.Thr101Met) variant causes a missense change. The variant allele was found at a frequency of 0.000194 in 1,614,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001676.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP12A | ENST00000381946.5 | c.302C>T | p.Thr101Met | missense_variant | Exon 4 of 23 | 1 | NM_001676.7 | ENSP00000371372.3 | ||
ATP12A | ENST00000218548.10 | c.302C>T | p.Thr101Met | missense_variant | Exon 4 of 23 | 1 | ENSP00000218548.6 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000116 AC: 29AN: 250476Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135454
GnomAD4 exome AF: 0.000198 AC: 289AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.000209 AC XY: 152AN XY: 727232
GnomAD4 genome AF: 0.000158 AC: 24AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.302C>T (p.T101M) alteration is located in exon 4 (coding exon 4) of the ATP12A gene. This alteration results from a C to T substitution at nucleotide position 302, causing the threonine (T) at amino acid position 101 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