Genetic Variant SLC3A2:c.760-41A>G (chr11-62884591-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001013251.3(SLC3A2):c.760-41A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 1,613,272 control chromosomes in the GnomAD database, including 622,349 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 0.80 ( 49999 hom., cov: 29)

Exomes 𝑓: 0.88 ( 572350 hom. )

Consequence

SLC3A2
NM_001013251.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.851

Publications

25 publications found

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 was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC3A2	NM_001013251.3 link	c.760-41A>G		intron_variant	Intron 4 of 8	ENST00000338663.12	NP_001013269.1	P08195-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC3A2	ENST00000338663.12 link	c.760-41A>G		intron_variant	Intron 4 of 8	1	NM_001013251.3	ENSP00000340815.7		P08195-2

Frequencies

GnomAD3 genomes

AF:

0.803

AC:

121976

AN:

151898

Hom.:

49979

Cov.:

show subpopulations

Gnomad AFR

AF:

0.640

Gnomad AMI

AF:

0.874

Gnomad AMR

AF:

0.729

Gnomad ASJ

AF:

0.799

Gnomad EAS

AF:

0.836

Gnomad SAS

AF:

0.869

Gnomad FIN

AF:

0.873

Gnomad MID

AF:

0.864

Gnomad NFE

AF:

0.899

Gnomad OTH

AF:

0.829

GnomAD2 exomes

AF:

0.841

AC:

211319

AN:

251170

AF XY:

0.853

show subpopulations

Gnomad AFR exome

AF:

0.632

Gnomad AMR exome

AF:

0.703

Gnomad ASJ exome

AF:

0.793

Gnomad EAS exome

AF:

0.831

Gnomad FIN exome

AF:

0.873

Gnomad NFE exome

AF:

0.901

Gnomad OTH exome

AF:

0.857

GnomAD4 exome

AF:

0.883

AC:

1290539

AN:

1461256

Hom.:

572350

Cov.:

AF XY:

0.884

AC XY:

642868

AN XY:

726904

show subpopulations

African (AFR)

AF:

0.635

AC:

21256

AN:

33454

American (AMR)

AF:

0.701

AC:

31308

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.792

AC:

20683

AN:

26122

East Asian (EAS)

AF:

0.829

AC:

32915

AN:

39684

South Asian (SAS)

AF:

0.884

AC:

76249

AN:

86228

European-Finnish (FIN)

AF:

0.880

AC:

46987

AN:

53416

Middle Eastern (MID)

AF:

0.871

AC:

5023

AN:

5768

European-Non Finnish (NFE)

AF:

0.903

AC:

1003469

AN:

1111540

Other (OTH)

AF:

0.872

AC:

52649

AN:

60374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

8333

16666

24999

33332

41665

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21388

42776

64164

85552

106940

<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:

0.803

AC:

122042

AN:

152016

Hom.:

49999

Cov.:

AF XY:

0.801

AC XY:

59513

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.640

AC:

26510

AN:

41422

American (AMR)

AF:

0.729

AC:

11120

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.799

AC:

2768

AN:

3466

East Asian (EAS)

AF:

0.836

AC:

4325

AN:

5174

South Asian (SAS)

AF:

0.870

AC:

4196

AN:

4822

European-Finnish (FIN)

AF:

0.873

AC:

9214

AN:

10560

Middle Eastern (MID)

AF:

0.864

AC:

254

AN:

294

European-Non Finnish (NFE)

AF:

0.899

AC:

61117

AN:

67994

Other (OTH)

AF:

0.825

AC:

1741

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1112

2223

3335

4446

5558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

868

1736

2604

3472

4340

<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:

0.868

Hom.:

124168

Bravo

AF:

0.787

Asia WGS

AF:

0.835

AC:

2907

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.42

(source)

DANN

Benign

0.48

PhyloP100

-0.85

RBP_binding_hub_radar

0.67

RBP_regulation_power_radar

2.0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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