dbSNP rs144685406: SLC3A2:p.Val12Ile (chr11-62856303-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001012662.3(SLC3A2):c.34G>A(p.Val12Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,144 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

SLC3A2
NM_001012662.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.26

Variant links:

Genes affected

SLC3A2 (HGNC:11026): (solute carrier family 3 member 2) This gene is a member of the solute carrier family and encodes a cell surface, transmembrane protein. The protein exists as the heavy chain of a heterodimer, covalently bound through di-sulfide bonds to one of several possible light chains. The encoded transporter plays a role in regulation of intracellular calcium levels and transports L-type amino acids. Alternatively spliced transcript variants, encoding different isoforms, have been characterized. [provided by RefSeq, Nov 2010]

SLC3A2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.09338772).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	Protein	UniProt
SLC3A2	NM_001012662.3 link	c.34G>A	p.Val12Ile	missense_variant	Exon 1 of 12	NP_001012680.1	P08195-5
SLC3A2	NM_002394.6 link	c.34G>A	p.Val12Ile	missense_variant	Exon 1 of 12	NP_002385.3	P08195-1
SLC3A2	NM_001012664.3 link	c.34G>A	p.Val12Ile	missense_variant	Exon 1 of 10	NP_001012682.1	P08195-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	Protein	UniProt
SLC3A2	ENST00000377890.6 link	c.34G>A	p.Val12Ile	missense_variant	Exon 1 of 12	1	ENSP00000367122.2	P08195-1
SLC3A2	ENST00000377889.6 link	c.34G>A	p.Val12Ile	missense_variant	Exon 1 of 10	1	ENSP00000367121.2	P08195-3
SLC3A2	ENST00000538084.2 link	c.34G>A	p.Val12Ile	missense_variant	Exon 1 of 13	3	ENSP00000440001.2	P08195-4H0YFS2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000398

AC:

AN:

251248

Hom.:

AF XY:

0.00000736

AC XY:

AN XY:

135790

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000880

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1461144

Hom.:

Cov.:

AF XY:

0.00000275

AC XY:

AN XY:

726728

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

0.0043

BayesDel_noAF

Benign

-0.23

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.20

T;.;.;.

Eigen

Benign

-0.90

Eigen_PC

Benign

-0.92

FATHMM_MKL

Benign

0.072

LIST_S2

Benign

0.59

T;T;T;T

M_CAP

Benign

0.084

MetaRNN

Benign

0.093

T;T;T;T

MetaSVM

Uncertain

0.46

MutationAssessor

Benign

0.0

N;.;N;.

PrimateAI

Benign

0.47

PROVEAN

Benign

-0.10

N;N;N;N

REVEL

Benign

0.17

Sift

Pathogenic

0.0

D;D;T;T

Sift4G

Benign

0.31

T;T;D;D

Polyphen

0.052

B;.;B;B

Vest4

0.17

MutPred

0.20

Loss of glycosylation at S14 (P = 0.1073);Loss of glycosylation at S14 (P = 0.1073);Loss of glycosylation at S14 (P = 0.1073);Loss of glycosylation at S14 (P = 0.1073);

MVP

0.31

MPC

0.54

ClinPred

0.34

GERP RS

2.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.10

gMVP

0.019

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over