rs5791053

Positions:

• chr11-35371110-G-GT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004171.4(SLC1A2):​c.17+47839_17+47840insA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.45 (16417 hom., cov: 0)
  • Exomes 𝑓: 0.49 (102830 hom.)
• Consequence: SLC1A2 NM_004171.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.15

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A2	NM_004171.4	c.17+47839_17+47840insA		intron_variant		ENST00000278379.9	NP_004162.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A2	ENST00000278379.9	c.17+47839_17+47840insA		intron_variant		1	NM_004171.4	ENSP00000278379	P4

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67917 AN: 151710 Hom.: 16406 Cov.: 0

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.472

GnomAD4 exome AF: 0.495 AC: 409988 AN: 828334 Hom.: 102830 Cov.: 2 AF XY: 0.496 AC XY: 189632 AN XY: 382652

Gnomad4 AFR exome AF: 0.251

Gnomad4 AMR exome AF: 0.569

Gnomad4 ASJ exome AF: 0.593

Gnomad4 EAS exome AF: 0.742

Gnomad4 SAS exome AF: 0.642

Gnomad4 FIN exome AF: 0.427

Gnomad4 NFE exome AF: 0.494

Gnomad4 OTH exome AF: 0.510

GnomAD4 genome AF: 0.448 AC: 67954 AN: 151828 Hom.: 16417 Cov.: 0 AF XY: 0.456 AC XY: 33872 AN XY: 74222

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.474

Alfa AF: 0.459 Hom.: 2011

Bravo AF: 0.449

Asia WGS AF: 0.620 AC: 2156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs5791053; hg19: chr11-35392657;