rs3838796

Positions:

• chr11-35277788-C-CT

Variant summary

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

The NM_004171.4(SLC1A2):​c.1421+3078_1421+3079insA 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 0.56 (24271 hom., cov: 0)
• Consequence: SLC1A2 NM_004171.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568

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 = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC1A2	NM_004171.4	c.1421+3078_1421+3079insA		intron_variant		ENST00000278379.9	NP_004162.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC1A2	ENST00000278379.9	c.1421+3078_1421+3079insA		intron_variant		1	NM_004171.4	ENSP00000278379.3

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84577 AN: 151880 Hom.: 24252 Cov.: 0

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.557 AC: 84642 AN: 152000 Hom.: 24271 Cov.: 0 AF XY: 0.564 AC XY: 41936 AN XY: 74294

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.580

Alfa AF: 0.567 Hom.: 3031

Bravo AF: 0.549

Asia WGS AF: 0.620 AC: 2152 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: rs3838796; hg19: chr11-35299335;