rs3774118

Variant names:

• chr3-10852326-C-T
• rs3774118
• NM_014229.3:c.756+7980C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014229.3(SLC6A11):​c.756+7980C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,252 control chromosomes in the GnomAD database, including 3,084 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 0.18 (3084 hom., cov: 33)
• Consequence: SLC6A11 NM_014229.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A11	NM_014229.3	c.756+7980C>T		intron_variant	Intron 5 of 13	ENST00000254488.7	NP_055044.1
SLC6A11	XM_047448764.1	c.234+7980C>T		intron_variant	Intron 3 of 11		XP_047304720.1
SLC6A11	XM_011534033.3	c.756+7980C>T		intron_variant	Intron 5 of 8		XP_011532335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A11	ENST00000254488.7	c.756+7980C>T		intron_variant	Intron 5 of 13	1	NM_014229.3	ENSP00000254488.2

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27623 AN: 152134 Hom.: 3082 Cov.: 33

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.194

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.181 AC: 27628 AN: 152252 Hom.: 3084 Cov.: 33 AF XY: 0.186 AC XY: 13833 AN XY: 74440

African (AFR) AF: 0.0642 AC: 2668 AN: 41546

American (AMR) AF: 0.153 AC: 2340 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1454 AN: 5162

South Asian (SAS) AF: 0.333 AC: 1607 AN: 4832

European-Finnish (FIN) AF: 0.244 AC: 2587 AN: 10612

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15180 AN: 68012

Other (OTH) AF: 0.192 AC: 405 AN: 2108

Alfa AF: 0.200 Hom.: 421

Bravo AF: 0.168

Asia WGS AF: 0.250 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.064
DANN	Benign	0.47
PhyloP100		-3.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3774118; hg19: chr3-10894011;