3-10830577-T-G

Variant names:

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

Variant summary

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

The NM_014229.3(SLC6A11):​c.623+7185T>G variant causes a intron 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_014229.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014229.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A11	NM_014229.3	MANE Select	c.623+7185T>G		intron	N/A	NP_055044.1
	SLC6A11	NM_001317406.3		c.*7181T>G		3_prime_UTR	Exon 4 of 4	NP_001304335.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A11	ENST00000254488.7	TSL:1 MANE Select	c.623+7185T>G		intron	N/A	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

African (AFR) AF: 0.817 AC: 33913 AN: 41486

American (AMR) AF: 0.591 AC: 9032 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1815 AN: 3468

East Asian (EAS) AF: 0.816 AC: 4206 AN: 5154

South Asian (SAS) AF: 0.780 AC: 3746 AN: 4802

European-Finnish (FIN) AF: 0.354 AC: 3726 AN: 10524

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27819 AN: 67886

Other (OTH) AF: 0.559 AC: 1177 AN: 2104

Alfa AF: 0.468 Hom.: 29711

Bravo AF: 0.595

Asia WGS AF: 0.800 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.76
DANN	Benign	0.77
PhyloP100		-0.74
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: rs971930; hg19: chr3-10872262;