Variant 3-10934163-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_014229.3(SLC6A11):c.1572C>T(p.Cys524=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0148 in 1,608,836 control chromosomes in the GnomAD database, including 944 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.015 ( 83 hom., cov: 32)

Exomes 𝑓: 0.015 ( 861 hom. )

Consequence

SLC6A11
NM_014229.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.457

Variant links:

Genes affected

SLC6A11 (HGNC:11044): (solute carrier family 6 member 11) The protein encoded by this gene is a sodium-dependent transporter that uptakes gamma-aminobutyric acid (GABA), an inhibitory neurotransmitter, which ends the GABA neurotransmission. Defects in this gene may result in epilepsy, behavioral problems, or intellectual problems. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]

SLC6A11 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP7

Synonymous conserved (PhyloP=-0.457 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A11	NM_014229.3 linkuse as main transcript	c.1572C>T	p.Cys524=	synonymous_variant	12/14	ENST00000254488.7
SLC6A11	XM_047448764.1 linkuse as main transcript	c.1050C>T	p.Cys350=	synonymous_variant	10/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A11	ENST00000254488.7 linkuse as main transcript	c.1572C>T	p.Cys524=	synonymous_variant	12/14	1	NM_014229.3	P1	P48066-1
	ENST00000656787.1 linkuse as main transcript	n.350+2827G>A		intron_variant, non_coding_transcript_variant
SLC6A11	ENST00000464828.1 linkuse as main transcript	n.198C>T		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes

AF:

0.0152

AC:

2315

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00915

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00667

Gnomad ASJ

AF:

0.00980

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.0638

Gnomad FIN

AF:

0.00914

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00770

Gnomad OTH

AF:

0.0120

GnomAD3 exomes

AF:

0.0258

AC:

6472

AN:

251082

Hom.:

333

AF XY:

0.0264

AC XY:

3580

AN XY:

135704

show subpopulations

Gnomad AFR exome

AF:

0.00867

Gnomad AMR exome

AF:

0.00819

Gnomad ASJ exome

AF:

0.00814

Gnomad EAS exome

AF:

0.170

Gnomad SAS exome

AF:

0.0563

Gnomad FIN exome

AF:

0.00828

Gnomad NFE exome

AF:

0.00726

Gnomad OTH exome

AF:

0.0170

GnomAD4 exome

AF:

0.0148

AC:

21548

AN:

1456586

Hom.:

861

Cov.:

AF XY:

0.0161

AC XY:

11650

AN XY:

725008

show subpopulations

Gnomad4 AFR exome

AF:

0.00731

Gnomad4 AMR exome

AF:

0.00767

Gnomad4 ASJ exome

AF:

0.00897

Gnomad4 EAS exome

AF:

0.176

Gnomad4 SAS exome

AF:

0.0564

Gnomad4 FIN exome

AF:

0.00877

Gnomad4 NFE exome

AF:

0.00653

Gnomad4 OTH exome

AF:

0.0189

GnomAD4 genome

AF:

0.0151

AC:

2306

AN:

152250

Hom.:

Cov.:

AF XY:

0.0169

AC XY:

1257

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.00917

Gnomad4 AMR

AF:

0.00667

Gnomad4 ASJ

AF:

0.00980

Gnomad4 EAS

AF:

0.162

Gnomad4 SAS

AF:

0.0630

Gnomad4 FIN

AF:

0.00914

Gnomad4 NFE

AF:

0.00771

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.00991

Hom.:

Bravo

AF:

0.0147

Asia WGS

AF:

0.120

AC:

417

AN:

3478

EpiCase

AF:

0.00710

EpiControl

AF:

0.00729

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

8.3

DANN

Benign

0.78

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over