X-139741069-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_001353812.2(ATP11C):c.3056C>T(p.Thr1019Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000749 in 1,201,009 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001353812.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP11C | NM_001353812.2 | c.3056C>T | p.Thr1019Met | missense_variant | 27/30 | ENST00000682941.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP11C | ENST00000682941.1 | c.3056C>T | p.Thr1019Met | missense_variant | 27/30 | NM_001353812.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000180 AC: 2AN: 111259Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33527
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181636Hom.: 0 AF XY: 0.0000150 AC XY: 1AN XY: 66506
GnomAD4 exome AF: 0.00000642 AC: 7AN: 1089750Hom.: 0 Cov.: 27 AF XY: 0.00000843 AC XY: 3AN XY: 356046
GnomAD4 genome ? AF: 0.0000180 AC: 2AN: 111259Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33527
ClinVar
Submissions by phenotype
X-linked congenital hemolytic anemia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at