chr3-11025190-A-T

Position:

• chr3-11025190-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003042.4(SLC6A1):​c.715-259A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 401,686 control chromosomes in the GnomAD database, including 4,369 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.16 (2505 hom., cov: 32)
  • Exomes 𝑓: 0.11 (1864 hom.)
• Consequence: SLC6A1 NM_003042.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.340

Genes affected

SLC6A1 (HGNC:11042): (solute carrier family 6 member 1) The protein encoded by this gene is a gamma-aminobutyric acid (GABA) transporter that localizes to the plasma membrane. The encoded protein removes GABA from the synaptic cleft, restoring it to presynaptic terminals. [provided by RefSeq, Jan 2017]

SLC6A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 3-11025190-A-T is Benign according to our data. Variant chr3-11025190-A-T is described in ClinVar as [Benign]. Clinvar id is 1261024.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A1	NM_003042.4	c.715-259A>T		intron_variant		ENST00000287766.10	NP_003033.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A1	ENST00000287766.10	c.715-259A>T		intron_variant		1	NM_003042.4	ENSP00000287766.4

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23821 AN: 152086 Hom.: 2503 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.150

GnomAD4 exome AF: 0.113 AC: 28249 AN: 249482 Hom.: 1864 Cov.: 3 AF XY: 0.113 AC XY: 14408 AN XY: 127634

Gnomad4 AFR exome AF: 0.292

Gnomad4 AMR exome AF: 0.0903

Gnomad4 ASJ exome AF: 0.147

Gnomad4 EAS exome AF: 0.126

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.0758

Gnomad4 NFE exome AF: 0.104

Gnomad4 OTH exome AF: 0.121

GnomAD4 genome AF: 0.157 AC: 23853 AN: 152204 Hom.: 2505 Cov.: 32 AF XY: 0.154 AC XY: 11489 AN XY: 74404

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0764

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0434 Hom.: 39

Bravo AF: 0.167

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.7
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: rs9822125; hg19: chr3-11066876;