Variant rs2304725 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.645T>C(p.Ser215Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 1,613,944 control chromosomes in the GnomAD database, including 93,608 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 0.33 ( 8399 hom., cov: 33)

Exomes 𝑓: 0.34 ( 85209 hom. )

Consequence

SLC6A11
NM_014229.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -6.71

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:

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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=-0.92).

BP7

Synonymous conserved (PhyloP=-6.71 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A11	NM_014229.3 linkuse as main transcript	c.645T>C	p.Ser215Ser	synonymous_variant	5/14	ENST00000254488.7	NP_055044.1	P48066-1
SLC6A11	XM_047448764.1 linkuse as main transcript	c.123T>C	p.Ser41Ser	synonymous_variant	3/12		XP_047304720.1
SLC6A11	XM_011534033.3 linkuse as main transcript	c.645T>C	p.Ser215Ser	synonymous_variant	5/9		XP_011532335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A11	ENST00000254488.7 linkuse as main transcript	c.645T>C	p.Ser215Ser	synonymous_variant	5/14	1	NM_014229.3	ENSP00000254488.2		P48066-1

Frequencies

GnomAD3 genomes

AF:

0.327

AC:

49706

AN:

152040

Hom.:

8394

Cov.:

show subpopulations

Gnomad AFR

AF:

0.321

Gnomad AMI

AF:

0.474

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.407

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.509

Gnomad FIN

AF:

0.309

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.327

Gnomad OTH

AF:

0.325

GnomAD3 exomes

AF:

0.341

AC:

85716

AN:

251176

Hom.:

15921

AF XY:

0.354

AC XY:

48031

AN XY:

135768

show subpopulations

Gnomad AFR exome

AF:

0.319

Gnomad AMR exome

AF:

0.181

Gnomad ASJ exome

AF:

0.407

Gnomad EAS exome

AF:

0.458

Gnomad SAS exome

AF:

0.511

Gnomad FIN exome

AF:

0.308

Gnomad NFE exome

AF:

0.329

Gnomad OTH exome

AF:

0.344

GnomAD4 exome

AF:

0.337

AC:

492583

AN:

1461786

Hom.:

85209

Cov.:

AF XY:

0.343

AC XY:

249412

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.321

Gnomad4 AMR exome

AF:

0.188

Gnomad4 ASJ exome

AF:

0.402

Gnomad4 EAS exome

AF:

0.418

Gnomad4 SAS exome

AF:

0.502

Gnomad4 FIN exome

AF:

0.309

Gnomad4 NFE exome

AF:

0.326

Gnomad4 OTH exome

AF:

0.359

GnomAD4 genome

AF:

0.327

AC:

49731

AN:

152158

Hom.:

8399

Cov.:

AF XY:

0.329

AC XY:

24506

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.321

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.407

Gnomad4 EAS

AF:

0.436

Gnomad4 SAS

AF:

0.510

Gnomad4 FIN

AF:

0.309

Gnomad4 NFE

AF:

0.327

Gnomad4 OTH

AF:

0.324

Alfa

AF:

0.337

Hom.:

23505

Bravo

AF:

0.319

Asia WGS

AF:

0.456

AC:

1589

AN:

3478

EpiCase

AF:

0.344

EpiControl

AF:

0.343

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.64

DANN

Benign

0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

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