Genetic Variant SLC3A2:c.425-217C>T (chr11-62881676-C-T) – 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.425-217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00525 in 862,040 control chromosomes in the GnomAD database, including 136 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 0.019 ( 92 hom., cov: 31)

Exomes 𝑓: 0.0022 ( 44 hom. )

Consequence

SLC3A2
NM_001013251.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.569

Publications

0 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=-0.73).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013251.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC3A2	NM_001013251.3	MANE Select	c.425-217C>T	intron	N/A	NP_001013269.1	P08195-2
SLC3A2	NM_001012662.3		c.731-217C>T	intron	N/A	NP_001012680.1	P08195-5
SLC3A2	NM_002394.6		c.728-217C>T	intron	N/A	NP_002385.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC3A2	ENST00000338663.12	TSL:1 MANE Select	c.425-217C>T	intron	N/A	ENSP00000340815.7	P08195-2
SLC3A2	ENST00000377890.6	TSL:1	c.728-217C>T	intron	N/A	ENSP00000367122.2	P08195-1
SLC3A2	ENST00000377889.6	TSL:1	c.542-217C>T	intron	N/A	ENSP00000367121.2	P08195-3

Frequencies

GnomAD3 genomes

AF:

0.0195

AC:

2958

AN:

151952

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0671

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00780

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000427

Gnomad OTH

AF:

0.0168

GnomAD4 exome

AF:

0.00221

AC:

1570

AN:

709970

Hom.:

Cov.:

AF XY:

0.00192

AC XY:

687

AN XY:

358412

show subpopulations

African (AFR)

AF:

0.0707

AC:

1215

AN:

17194

American (AMR)

AF:

0.00603

AC:

111

AN:

18412

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15200

East Asian (EAS)

AF:

0.00

AC:

AN:

31764

South Asian (SAS)

AF:

0.0000603

AC:

AN:

49754

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29750

Middle Eastern (MID)

AF:

0.00283

AC:

AN:

2474

European-Non Finnish (NFE)

AF:

0.000170

AC:

AN:

510942

Other (OTH)

AF:

0.00426

AC:

147

AN:

34480

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

164

245

327

409

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

150

<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:

0.0195

AC:

2960

AN:

152070

Hom.:

Cov.:

AF XY:

0.0189

AC XY:

1404

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.0670

AC:

2776

AN:

41460

American (AMR)

AF:

0.00772

AC:

118

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

5174

South Asian (SAS)

AF:

0.000208

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10586

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000427

AC:

AN:

67978

Other (OTH)

AF:

0.0166

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

134

267

401

534

668

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.0132

Hom.:

Bravo

AF:

0.0229

Asia WGS

AF:

0.00433

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

4.2

(source)

DANN

Benign

0.81

PhyloP100

-0.57

PromoterAI

-0.070

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over