3-57757682-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001377540.1(SLMAP):c.31C>T(p.Arg11Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,614,026 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 (★).
Frequency
Consequence
NM_001377540.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLMAP | NM_001377540.1 | c.31C>T | p.Arg11Cys | missense_variant | Exon 2 of 25 | ENST00000671191.1 | NP_001364469.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLMAP | ENST00000671191.1 | c.31C>T | p.Arg11Cys | missense_variant | Exon 2 of 25 | NM_001377540.1 | ENSP00000499458.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251386Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135888
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 727240
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152150Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
Brugada syndrome Uncertain:1
This variant has not been reported in the literature in individuals affected with SLMAP-related conditions. This variant is present in population databases (rs767298958, ExAC 0.05%). This sequence change replaces arginine with cysteine at codon 11 of the SLMAP protein (p.Arg11Cys). The arginine residue is moderately conserved and there is a large physicochemical difference between arginine and cysteine. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at