rs3838796

Variant names:

• chr11-35277788-C-CT
• rs3838796
• NM_004171.4:c.1421+3078_1421+3079insA

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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-AS1 (HGNC:40534): (SLC1A2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC1A2	NM_004171.4	c.1421+3078_1421+3079insA		intron_variant	Intron 9 of 10	ENST00000278379.9	NP_004162.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC1A2	ENST00000278379.9	c.1421+3078_1421+3079insA		intron_variant	Intron 9 of 10	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

African (AFR) AF: 0.403 AC: 16689 AN: 41458

American (AMR) AF: 0.630 AC: 9624 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3466

East Asian (EAS) AF: 0.635 AC: 3267 AN: 5148

South Asian (SAS) AF: 0.622 AC: 2996 AN: 4818

European-Finnish (FIN) AF: 0.622 AC: 6577 AN: 10574

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41180 AN: 67946

Other (OTH) AF: 0.580 AC: 1226 AN: 2112

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

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3838796; hg19: chr11-35299335;