rs901026

Variant names:

• chr3-10885597-T-A
• rs901026
• NM_014229.3:c.891+10502T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-10885597-T-A
• chr3-10885597-T-C
• chr3-10885597-T-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.891+10502T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 138,376 control chromosomes in the GnomAD database, including 2,895 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 0.19 (2895 hom., cov: 23)
• Consequence: SLC6A11 NM_014229.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 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.891+10502T>A		intron	N/A	NP_055044.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A11	ENST00000254488.7	TSL:1 MANE Select	c.891+10502T>A		intron	N/A	ENSP00000254488.2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 25626 AN: 138358 Hom.: 2893 Cov.: 23

Gnomad AFR AF: 0.0538

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.281

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.185 AC: 25629 AN: 138376 Hom.: 2895 Cov.: 23 AF XY: 0.185 AC XY: 12351 AN XY: 66724

African (AFR) AF: 0.0540 AC: 2057 AN: 38106

American (AMR) AF: 0.160 AC: 2276 AN: 14190

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1131 AN: 3246

East Asian (EAS) AF: 0.285 AC: 1326 AN: 4660

South Asian (SAS) AF: 0.286 AC: 1179 AN: 4128

European-Finnish (FIN) AF: 0.197 AC: 1638 AN: 8324

Middle Eastern (MID) AF: 0.286 AC: 75 AN: 262

European-Non Finnish (NFE) AF: 0.242 AC: 15200 AN: 62758

Other (OTH) AF: 0.219 AC: 410 AN: 1868

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.77
PhyloP100		0.25
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: rs901026; hg19: chr3-10927282;