rs12361171

Variant names:

• chr11-35256786-T-A
• rs12361171
• NM_004171.4:c.*4108A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-35256786-T-A
• chr11-35256786-T-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004171.4(SLC1A2):​c.*4108A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,260 control chromosomes in the GnomAD database, including 9,473 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 0.34 (9473 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SLC1A2 NM_004171.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 15 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004171.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A2	NM_004171.4	MANE Select	c.*4108A>T		3_prime_UTR	Exon 11 of 11	NP_004162.2
	SLC1A2	NM_001439342.1		c.*4108A>T		3_prime_UTR	Exon 11 of 11	NP_001426271.1
	SLC1A2	NM_001195728.3		c.*4108A>T		3_prime_UTR	Exon 12 of 12	NP_001182657.1	P43004-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC1A2	ENST00000278379.9	TSL:1 MANE Select	c.*4108A>T		3_prime_UTR	Exon 11 of 11	ENSP00000278379.3	P43004-1
	SLC1A2	ENST00000642769.1		c.*51-1978A>T		intron	N/A	ENSP00000493843.1	A0A2R8Y4N0
	SLC1A2	ENST00000647076.1		c.*51-1978A>T		intron	N/A	ENSP00000496759.1	A0A2R8YHI4

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50697 AN: 151140 Hom.: 9477 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.368

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.335 AC: 50693 AN: 151258 Hom.: 9473 Cov.: 31 AF XY: 0.341 AC XY: 25210 AN XY: 73822

African (AFR) AF: 0.164 AC: 6744 AN: 41202

American (AMR) AF: 0.351 AC: 5320 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3466

East Asian (EAS) AF: 0.474 AC: 2437 AN: 5146

South Asian (SAS) AF: 0.536 AC: 2570 AN: 4792

European-Finnish (FIN) AF: 0.345 AC: 3596 AN: 10438

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27051 AN: 67776

Other (OTH) AF: 0.367 AC: 768 AN: 2094

Alfa AF: 0.363 Hom.: 1299

Bravo AF: 0.324

Asia WGS AF: 0.439 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		0.036
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: rs12361171; hg19: chr11-35278333;