1-203683257-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001684.5(ATP2B4):c.52C>A(p.Arg18Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R18H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001684.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B4 | NM_001684.5 | c.52C>A | p.Arg18Ser | missense_variant | 2/21 | ENST00000357681.10 | |
ATP2B4 | NM_001001396.3 | c.52C>A | p.Arg18Ser | missense_variant | 2/22 | ||
ATP2B4 | NM_001365783.2 | c.52C>A | p.Arg18Ser | missense_variant | 2/21 | ||
ATP2B4 | NM_001365784.2 | c.52C>A | p.Arg18Ser | missense_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B4 | ENST00000357681.10 | c.52C>A | p.Arg18Ser | missense_variant | 2/21 | 1 | NM_001684.5 | A1 | |
ATP2B4 | ENST00000341360.7 | c.52C>A | p.Arg18Ser | missense_variant | 2/22 | 1 | P4 | ||
ATP2B4 | ENST00000705901.1 | c.52C>A | p.Arg18Ser | missense_variant | 2/21 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461872Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 727236
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2022 | The c.52C>A (p.R18S) alteration is located in exon 2 (coding exon 1) of the ATP2B4 gene. This alteration results from a C to A substitution at nucleotide position 52, causing the arginine (R) at amino acid position 18 to be replaced by a serine (S). 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