11-35259553-A-T

Position:

• chr11-35259553-A-T

Variant summary

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

The NM_004171.4(SLC1A2):​c.*1341T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,220 control chromosomes in the GnomAD database, including 9,285 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 0.33 (9282 hom., cov: 33)
  • Exomes 𝑓: 0.36 (3 hom.)
• Consequence: SLC1A2 NM_004171.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC1A2	NM_004171.4	c.*1341T>A		3_prime_UTR_variant	11/11	ENST00000278379.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC1A2	ENST00000278379.9	c.*1341T>A		3_prime_UTR_variant	11/11	1	NM_004171.4	P4

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49515 AN: 152046 Hom.: 9287 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.361

GnomAD4 exome AF: 0.357 AC: 20 AN: 56 Hom.: 3 Cov.: 0 AF XY: 0.367 AC XY: 11 AN XY: 30

Gnomad4 FIN exome AF: 0.352

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.325 AC: 49508 AN: 152164 Hom.: 9282 Cov.: 33 AF XY: 0.332 AC XY: 24696 AN XY: 74392

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.359

Alfa AF: 0.358 Hom.: 1284

Bravo AF: 0.314

Asia WGS AF: 0.438 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.90
DANN	Benign	0.46

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: rs10742339; hg19: chr11-35281100;