rs3794099

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004171.4(SLC1A2):​c.1421+7054T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,056 control chromosomes in the GnomAD database, including 11,154 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 0.38 ( 11154 hom., cov: 32)

Consequence

SLC1A2
NM_004171.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.516 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC1A2NM_004171.4 linkc.1421+7054T>C intron_variant Intron 9 of 10 ENST00000278379.9 NP_004162.2 P43004-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC1A2ENST00000278379.9 linkc.1421+7054T>C intron_variant Intron 9 of 10 1 NM_004171.4 ENSP00000278379.3 P43004-1

Frequencies

GnomAD3 genomes
AF:
0.380
AC:
57670
AN:
151936
Hom.:
11152
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.326
Gnomad AMI
AF:
0.518
Gnomad AMR
AF:
0.368
Gnomad ASJ
AF:
0.465
Gnomad EAS
AF:
0.431
Gnomad SAS
AF:
0.531
Gnomad FIN
AF:
0.343
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.398
Gnomad OTH
AF:
0.399
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.379
AC:
57696
AN:
152056
Hom.:
11154
Cov.:
32
AF XY:
0.384
AC XY:
28543
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.326
Gnomad4 AMR
AF:
0.367
Gnomad4 ASJ
AF:
0.465
Gnomad4 EAS
AF:
0.430
Gnomad4 SAS
AF:
0.533
Gnomad4 FIN
AF:
0.343
Gnomad4 NFE
AF:
0.398
Gnomad4 OTH
AF:
0.396
Alfa
AF:
0.385
Hom.:
1913
Bravo
AF:
0.375
Asia WGS
AF:
0.441
AC:
1529
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.47
DANN
Benign
0.69

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3794099; hg19: chr11-35295360; API