chr3-11029285-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP6_ModerateBS2
The NM_003042.4(SLC6A1):c.1256G>A(p.Arg419His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,758 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R419C) has been classified as Uncertain significance.
Frequency
Consequence
NM_003042.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A1 | NM_003042.4 | c.1256G>A | p.Arg419His | missense_variant | 12/16 | ENST00000287766.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A1 | ENST00000287766.10 | c.1256G>A | p.Arg419His | missense_variant | 12/16 | 1 | NM_003042.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248982Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134508
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460620Hom.: 0 Cov.: 32 AF XY: 0.00000964 AC XY: 7AN XY: 726518
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74310
ClinVar
Submissions by phenotype
Myoclonic-atonic epilepsy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at