rs116620331
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003042.4(SLC6A1):c.480G>A(p.Pro160=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000089 in 1,459,992 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P160P) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A1 | NM_003042.4 | c.480G>A | p.Pro160= | synonymous_variant | 6/16 | ENST00000287766.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A1 | ENST00000287766.10 | c.480G>A | p.Pro160= | synonymous_variant | 6/16 | 1 | NM_003042.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249366Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134720
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1459992Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 726186
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Myoclonic-atonic epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at