chr1-203698330-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001684.5(ATP2B4):c.367C>T(p.Arg123Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000681 in 1,614,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R123H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001684.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B4 | NM_001684.5 | c.367C>T | p.Arg123Cys | missense_variant | 3/21 | ENST00000357681.10 | |
ATP2B4 | NM_001001396.3 | c.367C>T | p.Arg123Cys | missense_variant | 3/22 | ||
ATP2B4 | NM_001365783.2 | c.367C>T | p.Arg123Cys | missense_variant | 3/21 | ||
ATP2B4 | NM_001365784.2 | c.367C>T | p.Arg123Cys | missense_variant | 3/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B4 | ENST00000357681.10 | c.367C>T | p.Arg123Cys | missense_variant | 3/21 | 1 | NM_001684.5 | A1 | |
ATP2B4 | ENST00000341360.7 | c.367C>T | p.Arg123Cys | missense_variant | 3/22 | 1 | P4 | ||
ATP2B4 | ENST00000705901.1 | c.367C>T | p.Arg123Cys | missense_variant | 3/21 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152106Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251414Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135872
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461870Hom.: 0 Cov.: 35 AF XY: 0.0000839 AC XY: 61AN XY: 727234
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.367C>T (p.R123C) alteration is located in exon 3 (coding exon 2) of the ATP2B4 gene. This alteration results from a C to T substitution at nucleotide position 367, causing the arginine (R) at amino acid position 123 to be replaced by a cysteine (C). 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