chr2-40428505-A-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_021097.5(SLC8A1):c.1776T>G(p.Cys592Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,458,036 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021097.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC8A1 | NM_021097.5 | c.1776T>G | p.Cys592Trp | missense_variant | 2/11 | ENST00000332839.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC8A1 | ENST00000332839.9 | c.1776T>G | p.Cys592Trp | missense_variant | 2/11 | 1 | NM_021097.5 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000810 AC: 2AN: 246900Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133308
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1458036Hom.: 0 Cov.: 35 AF XY: 0.0000110 AC XY: 8AN XY: 725174
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.1776T>G (p.C592W) alteration is located in exon 1 (coding exon 1) of the SLC8A1 gene. This alteration results from a T to G substitution at nucleotide position 1776, causing the cysteine (C) at amino acid position 592 to be replaced by a tryptophan (W). 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