3-10830577-T-G

Variant names:

• chr3-10830577-T-G
• rs971930
• NM_014229.3:c.623+7185T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001317406.3(SLC6A11):​c.*7181T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,904 control chromosomes in the GnomAD database, including 27,156 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 0.57 (27156 hom., cov: 32)
• Consequence: SLC6A11 NM_001317406.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A11	NM_014229.3	c.623+7185T>G		intron_variant	Intron 4 of 13	ENST00000254488.7	NP_055044.1
SLC6A11	NM_001317406.3	c.*7181T>G		3_prime_UTR_variant	Exon 4 of 4		NP_001304335.1
SLC6A11	XM_047448764.1	c.46+7185T>G		intron_variant	Intron 1 of 11		XP_047304720.1
SLC6A11	XM_011534033.3	c.623+7185T>G		intron_variant	Intron 4 of 8		XP_011532335.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A11	ENST00000254488.7	c.623+7185T>G		intron_variant	Intron 4 of 13	1	NM_014229.3	ENSP00000254488.2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86001 AN: 151786 Hom.: 27106 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.567 AC: 86111 AN: 151904 Hom.: 27156 Cov.: 32 AF XY: 0.571 AC XY: 42372 AN XY: 74234

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.354

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.559

Alfa AF: 0.456 Hom.: 22130

Bravo AF: 0.595

Asia WGS AF: 0.800 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.76
DANN	Benign	0.77

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

Other links and lift over

dbSNP: rs971930; hg19: chr3-10872262;