3-57922980-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001377540.1(SLMAP):c.2402A>G(p.Gln801Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000129 in 1,614,038 control chromosomes in the GnomAD database, including 2 homozygotes. 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLMAP | NM_001377540.1 | c.2402A>G | p.Gln801Arg | missense_variant | Exon 23 of 25 | ENST00000671191.1 | NP_001364469.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLMAP | ENST00000671191.1 | c.2402A>G | p.Gln801Arg | missense_variant | Exon 23 of 25 | NM_001377540.1 | ENSP00000499458.1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 250894Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135612
GnomAD4 exome AF: 0.000138 AC: 201AN: 1461676Hom.: 2 Cov.: 31 AF XY: 0.000135 AC XY: 98AN XY: 727140
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152362Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2300A>G (p.Q767R) alteration is located in exon 20 (coding exon 20) of the SLMAP gene. This alteration results from a A to G substitution at nucleotide position 2300, causing the glutamine (Q) at amino acid position 767 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Brugada syndrome Uncertain:1
This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 767 of the SLMAP protein (p.Gln767Arg). This variant is present in population databases (rs142778041, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with SLMAP-related conditions. ClinVar contains an entry for this variant (Variation ID: 532119). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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. -
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at