rs35513423

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The ENST00000287766.10(SLC6A1):ā€‹c.1002A>Gā€‹(p.Ala334=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0017 in 1,613,596 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.0094 ( 28 hom., cov: 32)
Exomes š‘“: 0.00090 ( 14 hom. )

Consequence

SLC6A1
ENST00000287766.10 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -1.32
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 3-11026283-A-G is Benign according to our data. Variant chr3-11026283-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 475465.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.32 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00941 (1428/151770) while in subpopulation AFR AF= 0.0331 (1367/41312). AF 95% confidence interval is 0.0316. There are 28 homozygotes in gnomad4. There are 667 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1428 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC6A1NM_003042.4 linkuse as main transcriptc.1002A>G p.Ala334= synonymous_variant 10/16 ENST00000287766.10 NP_003033.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC6A1ENST00000287766.10 linkuse as main transcriptc.1002A>G p.Ala334= synonymous_variant 10/161 NM_003042.4 ENSP00000287766 P1

Frequencies

GnomAD3 genomes
AF:
0.00938
AC:
1423
AN:
151654
Hom.:
28
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0331
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00768
GnomAD3 exomes
AF:
0.00256
AC:
643
AN:
251418
Hom.:
9
AF XY:
0.00178
AC XY:
242
AN XY:
135888
show subpopulations
Gnomad AFR exome
AF:
0.0350
Gnomad AMR exome
AF:
0.00176
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000703
Gnomad OTH exome
AF:
0.000652
GnomAD4 exome
AF:
0.000900
AC:
1315
AN:
1461826
Hom.:
14
Cov.:
32
AF XY:
0.000745
AC XY:
542
AN XY:
727218
show subpopulations
Gnomad4 AFR exome
AF:
0.0331
Gnomad4 AMR exome
AF:
0.00183
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000928
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000144
Gnomad4 OTH exome
AF:
0.00162
GnomAD4 genome
AF:
0.00941
AC:
1428
AN:
151770
Hom.:
28
Cov.:
32
AF XY:
0.00899
AC XY:
667
AN XY:
74156
show subpopulations
Gnomad4 AFR
AF:
0.0331
Gnomad4 AMR
AF:
0.00262
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00760
Alfa
AF:
0.00536
Hom.:
4
Bravo
AF:
0.0101
Asia WGS
AF:
0.000866
AC:
3
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsJun 18, 2020- -
SLC6A1-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 09, 2021This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitterclinical testingAmbry GeneticsApr 18, 2016This 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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 28, 2024- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 20, 2019- -
Myoclonic-astatic epilepsy Benign:1
Likely benign, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsJan 24, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
1.1
DANN
Benign
0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35513423; hg19: chr3-11067969; API