Genetic Variant SLC3A2:c.424+123T>C (chr11-62881570-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_001013251.3(SLC3A2):c.424+123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,299,680 control chromosomes in the GnomAD database, including 49,802 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 0.20 ( 3807 hom., cov: 29)

Exomes 𝑓: 0.28 ( 45995 hom. )

Consequence

SLC3A2
NM_001013251.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.841

Publications

8 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:

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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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC3A2	NM_001013251.3 link	c.424+123T>C		intron_variant	Intron 1 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.424+123T>C		intron_variant	Intron 1 of 8	1	NM_001013251.3	ENSP00000340815.7		P08195-2

Frequencies

GnomAD3 genomes

AF:

0.205

AC:

30623

AN:

149686

Hom.:

3804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0677

Gnomad AMI

AF:

0.272

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.116

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.249

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.225

GnomAD4 exome

AF:

0.277

AC:

318233

AN:

1149878

Hom.:

45995

Cov.:

AF XY:

0.274

AC XY:

153727

AN XY:

560512

show subpopulations

African (AFR)

AF:

0.0612

AC:

1588

AN:

25968

American (AMR)

AF:

0.168

AC:

3403

AN:

20252

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

3878

AN:

17966

East Asian (EAS)

AF:

0.159

AC:

5347

AN:

33720

South Asian (SAS)

AF:

0.191

AC:

11549

AN:

60424

European-Finnish (FIN)

AF:

0.270

AC:

8045

AN:

29838

Middle Eastern (MID)

AF:

0.194

AC:

643

AN:

3314

European-Non Finnish (NFE)

AF:

0.298

AC:

271250

AN:

909472

Other (OTH)

AF:

0.256

AC:

12530

AN:

48924

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

11182

22365

33547

44730

55912

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8872

17744

26616

35488

44360

<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:

0.204

AC:

30619

AN:

149802

Hom.:

3807

Cov.:

AF XY:

0.202

AC XY:

14731

AN XY:

73048

show subpopulations

African (AFR)

AF:

0.0674

AC:

2756

AN:

40870

American (AMR)

AF:

0.181

AC:

2722

AN:

15012

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

750

AN:

3454

East Asian (EAS)

AF:

0.115

AC:

581

AN:

5034

South Asian (SAS)

AF:

0.182

AC:

857

AN:

4720

European-Finnish (FIN)

AF:

0.249

AC:

2548

AN:

10224

Middle Eastern (MID)

AF:

0.224

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.292

AC:

19631

AN:

67216

Other (OTH)

AF:

0.223

AC:

464

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

1029

2059

3088

4118

5147

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

322

644

966

1288

1610

<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:

0.257

Hom.:

15706

Bravo

AF:

0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.5

(source)

DANN

Benign

0.51

PhyloP100

0.84

PromoterAI

-0.043

Neutral

(source)

Mutation Taster

=99/1

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