Variant 11-35317346-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004171.4(SLC1A2):c.157+31C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 1,602,160 control chromosomes in the GnomAD database, including 41,850 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3423 hom., cov: 32)

Exomes 𝑓: 0.23 ( 38427 hom. )

Consequence

SLC1A2
NM_004171.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0770

Variant links:

Genes affected

SLC1A2 (HGNC:10940): (solute carrier family 1 member 2) This gene encodes a member of a family of solute transporter proteins. The membrane-bound protein is the principal transporter that clears the excitatory neurotransmitter glutamate from the extracellular space at synapses in the central nervous system. Glutamate clearance is necessary for proper synaptic activation and to prevent neuronal damage from excessive activation of glutamate receptors. Improper regulation of this gene is thought to be associated with several neurological disorders. Alternatively spliced transcript variants of this gene have been identified. [provided by RefSeq, Jun 2017]

SLC1A2 links:

SLC1A2 (HGNC:):

SLC1A2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 11-35317346-G-C is Benign according to our data. Variant chr11-35317346-G-C is described in ClinVar as [Benign]. Clinvar id is 1332978.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A2	NM_004171.4 linkuse as main transcript	c.157+31C>G		intron_variant		ENST00000278379.9	NP_004162.2	P43004-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A2	ENST00000278379.9 linkuse as main transcript	c.157+31C>G		intron_variant		1	NM_004171.4	ENSP00000278379.3		P43004-1

Frequencies

GnomAD3 genomes

AF:

0.195

AC:

29664

AN:

152070

Hom.:

3404

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0800

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.0933

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.195

GnomAD3 exomes

AF:

0.219

AC:

53505

AN:

244394

Hom.:

6247

AF XY:

0.213

AC XY:

28200

AN XY:

132184

show subpopulations

Gnomad AFR exome

AF:

0.0747

Gnomad AMR exome

AF:

0.290

Gnomad ASJ exome

AF:

0.259

Gnomad EAS exome

AF:

0.202

Gnomad SAS exome

AF:

0.101

Gnomad FIN exome

AF:

0.279

Gnomad NFE exome

AF:

0.237

Gnomad OTH exome

AF:

0.249

GnomAD4 exome

AF:

0.226

AC:

327107

AN:

1449972

Hom.:

38427

Cov.:

AF XY:

0.222

AC XY:

159654

AN XY:

719306

show subpopulations

Gnomad4 AFR exome

AF:

0.0762

Gnomad4 AMR exome

AF:

0.285

Gnomad4 ASJ exome

AF:

0.261

Gnomad4 EAS exome

AF:

0.267

Gnomad4 SAS exome

AF:

0.103

Gnomad4 FIN exome

AF:

0.276

Gnomad4 NFE exome

AF:

0.233

Gnomad4 OTH exome

AF:

0.212

GnomAD4 genome

AF:

0.195

AC:

29703

AN:

152188

Hom.:

3423

Cov.:

AF XY:

0.197

AC XY:

14657

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.0798

Gnomad4 AMR

AF:

0.269

Gnomad4 ASJ

AF:

0.251

Gnomad4 EAS

AF:

0.208

Gnomad4 SAS

AF:

0.0927

Gnomad4 FIN

AF:

0.287

Gnomad4 NFE

AF:

0.238

Gnomad4 OTH

AF:

0.203

Alfa

AF:

0.151

Hom.:

453

Bravo

AF:

0.191

Asia WGS

AF:

0.181

AC:

629

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Developmental and epileptic encephalopathy, 41

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.1

DANN

Benign

0.37

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over