1-203683210-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001684.5(ATP2B4):c.5C>T(p.Thr2Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000473 in 1,613,070 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001684.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP2B4 | NM_001684.5 | c.5C>T | p.Thr2Met | missense_variant | Exon 2 of 21 | ENST00000357681.10 | NP_001675.3 | |
ATP2B4 | NM_001001396.3 | c.5C>T | p.Thr2Met | missense_variant | Exon 2 of 22 | NP_001001396.1 | ||
ATP2B4 | NM_001365783.2 | c.5C>T | p.Thr2Met | missense_variant | Exon 2 of 21 | NP_001352712.1 | ||
ATP2B4 | NM_001365784.2 | c.5C>T | p.Thr2Met | missense_variant | Exon 2 of 21 | NP_001352713.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP2B4 | ENST00000357681.10 | c.5C>T | p.Thr2Met | missense_variant | Exon 2 of 21 | 1 | NM_001684.5 | ENSP00000350310.5 | ||
ATP2B4 | ENST00000341360.7 | c.5C>T | p.Thr2Met | missense_variant | Exon 2 of 22 | 1 | ENSP00000340930.2 | |||
ATP2B4 | ENST00000705901.1 | c.5C>T | p.Thr2Met | missense_variant | Exon 2 of 21 | ENSP00000516177.1 |
Frequencies
GnomAD3 genomes AF: 0.000506 AC: 77AN: 152166Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000971 AC: 243AN: 250326Hom.: 0 AF XY: 0.000850 AC XY: 115AN XY: 135234
GnomAD4 exome AF: 0.000470 AC: 686AN: 1460786Hom.: 5 Cov.: 29 AF XY: 0.000454 AC XY: 330AN XY: 726608
GnomAD4 genome AF: 0.000506 AC: 77AN: 152284Hom.: 1 Cov.: 32 AF XY: 0.000484 AC XY: 36AN XY: 74446
ClinVar
Submissions by phenotype
ATP2B4-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at