NM_003042.4:c.31G>A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_003042.4(SLC6A1):c.31G>A(p.Gly11Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,726 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003042.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A1 | NM_003042.4 | c.31G>A | p.Gly11Arg | missense_variant | Exon 3 of 16 | ENST00000287766.10 | NP_003033.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151950Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 250956Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135768
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727188
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151950Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74210
ClinVar
Submissions by phenotype
Epilepsy with myoclonic atonic seizures Uncertain:2Benign:1
The c.31G>A(p.Gly11Arg) missense variant in exon 3 of 16 of SLC6A1 has not been reported in affected individuals in the available literature. This variant is seen at a very low frequency in in gnomADv3 (4 heterozygotes, allele frequency =0.00002632, no homozygotes) indicating it is not a common benign variant in the populations represented in this database. In silico predictors suggest this variant is benign (REVEL; score:0.4429) and tolerated (SIFT; score:0.17). Given the lack of inheritance data and functional studies supporting its pathogenicity, the c.31G>A(p.Gly11Arg) variant identified in the SLC6A1 gene is reported here as a Variant of Uncertain Significance. -
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Inborn genetic diseases Uncertain:1
The p.G11R variant (also known as c.31G>A), located in coding exon 1 of the SLC6A1 gene, results from a G to A substitution at nucleotide position 31. The glycine at codon 11 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at