1-203683224-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001684.5(ATP2B4):c.19C>A(p.Arg7Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00231 in 1,613,910 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R7C) has been classified as Likely benign.
Frequency
Consequence
NM_001684.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B4 | NM_001684.5 | c.19C>A | p.Arg7Ser | missense_variant | 2/21 | ENST00000357681.10 | |
ATP2B4 | NM_001001396.3 | c.19C>A | p.Arg7Ser | missense_variant | 2/22 | ||
ATP2B4 | NM_001365783.2 | c.19C>A | p.Arg7Ser | missense_variant | 2/21 | ||
ATP2B4 | NM_001365784.2 | c.19C>A | p.Arg7Ser | missense_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B4 | ENST00000357681.10 | c.19C>A | p.Arg7Ser | missense_variant | 2/21 | 1 | NM_001684.5 | A1 | |
ATP2B4 | ENST00000341360.7 | c.19C>A | p.Arg7Ser | missense_variant | 2/22 | 1 | P4 | ||
ATP2B4 | ENST00000705901.1 | c.19C>A | p.Arg7Ser | missense_variant | 2/21 |
Frequencies
GnomAD3 genomes AF: 0.00422 AC: 642AN: 152144Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00561 AC: 1409AN: 251060Hom.: 29 AF XY: 0.00518 AC XY: 703AN XY: 135670
GnomAD4 exome AF: 0.00211 AC: 3083AN: 1461648Hom.: 51 Cov.: 29 AF XY: 0.00196 AC XY: 1426AN XY: 727134
GnomAD4 genome AF: 0.00423 AC: 644AN: 152262Hom.: 14 Cov.: 32 AF XY: 0.00623 AC XY: 464AN XY: 74432
ClinVar
Submissions by phenotype
ATP2B4-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | 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
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at