3-11022405-G-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003042.4(SLC6A1):c.651G>T(p.Thr217Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0479 in 1,613,392 control chromosomes in the GnomAD database, including 2,298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T217T) has been classified as Likely benign.
Frequency
Consequence
NM_003042.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A1 | NM_003042.4 | c.651G>T | p.Thr217Thr | synonymous_variant | 7/16 | ENST00000287766.10 | NP_003033.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0413 AC: 6279AN: 152206Hom.: 173 Cov.: 33
GnomAD3 exomes AF: 0.0509 AC: 12717AN: 249628Hom.: 485 AF XY: 0.0558 AC XY: 7527AN XY: 134884
GnomAD4 exome AF: 0.0485 AC: 70931AN: 1461068Hom.: 2126 Cov.: 31 AF XY: 0.0512 AC XY: 37225AN XY: 726752
GnomAD4 genome AF: 0.0412 AC: 6278AN: 152324Hom.: 172 Cov.: 33 AF XY: 0.0418 AC XY: 3116AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 21, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Epilepsy with myoclonic atonic seizures Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 04, 2025 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 15, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at