rs33948309
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003042.4(SLC6A1):c.780G>A(p.Thr260=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0035 in 1,614,052 control chromosomes in the GnomAD database, including 155 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.019 ( 98 hom., cov: 32)
Exomes 𝑓: 0.0019 ( 57 hom. )
Consequence
SLC6A1
NM_003042.4 synonymous
NM_003042.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.995
Genes affected
SLC6A1 (HGNC:11042): (solute carrier family 6 member 1) The protein encoded by this gene is a gamma-aminobutyric acid (GABA) transporter that localizes to the plasma membrane. The encoded protein removes GABA from the synaptic cleft, restoring it to presynaptic terminals. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 3-11025514-G-A is Benign according to our data. Variant chr3-11025514-G-A is described in ClinVar as [Benign]. Clinvar id is 475490.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.995 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0634 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A1 | NM_003042.4 | c.780G>A | p.Thr260= | synonymous_variant | 8/16 | ENST00000287766.10 | NP_003033.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A1 | ENST00000287766.10 | c.780G>A | p.Thr260= | synonymous_variant | 8/16 | 1 | NM_003042.4 | ENSP00000287766 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0189 AC: 2877AN: 152106Hom.: 98 Cov.: 32
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GnomAD3 exomes AF: 0.00481 AC: 1208AN: 251360Hom.: 30 AF XY: 0.00343 AC XY: 466AN XY: 135842
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GnomAD4 exome AF: 0.00190 AC: 2773AN: 1461828Hom.: 57 Cov.: 31 AF XY: 0.00165 AC XY: 1198AN XY: 727218
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GnomAD4 genome AF: 0.0189 AC: 2880AN: 152224Hom.: 98 Cov.: 32 AF XY: 0.0182 AC XY: 1351AN XY: 74428
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 17, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 07, 2017 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 17, 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. - |
Myoclonic-atonic epilepsy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at