dbSNP rs1570216: SLC1A2:c.*107A>G (chr11-35260787-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004171.4(SLC1A2):c.*107A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 828,966 control chromosomes in the GnomAD database, including 7,401 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 0.12 ( 1122 hom., cov: 33)

Exomes 𝑓: 0.13 ( 6279 hom. )

Consequence

SLC1A2
NM_004171.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.977

Publications

15 publications found

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]

SLC1A2 links:

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

SLC1A2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC1A2	NM_004171.4 link	c.*107A>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000278379.9	NP_004162.2	P43004-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC1A2	ENST00000278379.9 link	c.*107A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_004171.4	ENSP00000278379.3		P43004-1

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17601

AN:

152170

Hom.:

1106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0688

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.0681

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.128

Gnomad OTH

AF:

0.127

GnomAD4 exome

AF:

0.131

AC:

88632

AN:

676678

Hom.:

6279

Cov.:

AF XY:

0.127

AC XY:

45888

AN XY:

360122

show subpopulations

African (AFR)

AF:

0.0701

AC:

1213

AN:

17312

American (AMR)

AF:

0.182

AC:

6457

AN:

35572

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

2660

AN:

20254

East Asian (EAS)

AF:

0.211

AC:

7106

AN:

33652

South Asian (SAS)

AF:

0.0768

AC:

4930

AN:

64168

European-Finnish (FIN)

AF:

0.138

AC:

6469

AN:

47046

Middle Eastern (MID)

AF:

0.109

AC:

449

AN:

4110

European-Non Finnish (NFE)

AF:

0.131

AC:

55016

AN:

420368

Other (OTH)

AF:

0.127

AC:

4332

AN:

34196

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3767

7534

11300

15067

18834

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

958

1916

2874

3832

4790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.116

AC:

17648

AN:

152288

Hom.:

1122

Cov.:

AF XY:

0.117

AC XY:

8711

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.0690

AC:

2868

AN:

41564

American (AMR)

AF:

0.179

AC:

2734

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.124

AC:

429

AN:

3470

East Asian (EAS)

AF:

0.153

AC:

792

AN:

5184

South Asian (SAS)

AF:

0.0678

AC:

327

AN:

4826

European-Finnish (FIN)

AF:

0.133

AC:

1412

AN:

10602

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.128

AC:

8707

AN:

68014

Other (OTH)

AF:

0.135

AC:

285

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

819

1639

2458

3278

4097

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.127

Hom.:

5841

Bravo

AF:

0.119

Asia WGS

AF:

0.150

AC:

522

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.2

(source)

DANN

Benign

0.42

PhyloP100

-0.98

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over