dbSNP rs12703774: SLC37A3:c.882+10G>A (chr7-140351263-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_207113.3(SLC37A3):c.882+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 1,608,512 control chromosomes in the GnomAD database, including 161,070 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 0.41 ( 13137 hom., cov: 32)

Exomes 𝑓: 0.45 ( 147933 hom. )

Consequence

SLC37A3
NM_207113.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

12 publications found

Variant links:

Genes affected

SLC37A3 (HGNC:20651): (solute carrier family 37 member 3) Predicted to enable transmembrane transporter activity. Predicted to be involved in carbohydrate transport and transmembrane transport. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC37A3 Gene-Disease associations (from GenCC):

retinitis pigmentosa
Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics

SLC37A3 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 (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC37A3	NM_207113.3 link	c.882+10G>A		intron_variant	Intron 9 of 14	ENST00000326232.14	NP_996996.1	Q8NCC5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC37A3	ENST00000326232.14 link	c.882+10G>A		intron_variant	Intron 9 of 14	1	NM_207113.3	ENSP00000321498.9		Q8NCC5-1

Frequencies

GnomAD3 genomes

AF:

0.410

AC:

62336

AN:

151954

Hom.:

13137

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.468

Gnomad AMR

AF:

0.397

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.434

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.446

Gnomad MID

AF:

0.427

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.412

GnomAD2 exomes

AF:

0.429

AC:

106479

AN:

248216

AF XY:

0.429

show subpopulations

Gnomad AFR exome

AF:

0.318

Gnomad AMR exome

AF:

0.403

Gnomad ASJ exome

AF:

0.401

Gnomad EAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.447

Gnomad NFE exome

AF:

0.458

Gnomad OTH exome

AF:

0.448

GnomAD4 exome

AF:

0.449

AC:

654052

AN:

1456440

Hom.:

147933

Cov.:

AF XY:

0.448

AC XY:

324243

AN XY:

724464

show subpopulations

African (AFR)

AF:

0.321

AC:

10694

AN:

33324

American (AMR)

AF:

0.399

AC:

17656

AN:

44226

Ashkenazi Jewish (ASJ)

AF:

0.404

AC:

10475

AN:

25918

East Asian (EAS)

AF:

0.402

AC:

15947

AN:

39650

South Asian (SAS)

AF:

0.394

AC:

33771

AN:

85780

European-Finnish (FIN)

AF:

0.449

AC:

23957

AN:

53302

Middle Eastern (MID)

AF:

0.430

AC:

2469

AN:

5744

European-Non Finnish (NFE)

AF:

0.462

AC:

512336

AN:

1108316

Other (OTH)

AF:

0.444

AC:

26747

AN:

60180

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

16773

33547

50320

67094

83867

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15256

30512

45768

61024

76280

<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:

0.410

AC:

62369

AN:

152072

Hom.:

13137

Cov.:

AF XY:

0.411

AC XY:

30522

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.322

AC:

13338

AN:

41482

American (AMR)

AF:

0.397

AC:

6061

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

1382

AN:

3472

East Asian (EAS)

AF:

0.433

AC:

2242

AN:

5172

South Asian (SAS)

AF:

0.396

AC:

1905

AN:

4816

European-Finnish (FIN)

AF:

0.446

AC:

4720

AN:

10582

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.460

AC:

31298

AN:

67966

Other (OTH)

AF:

0.413

AC:

870

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1899

3798

5698

7597

9496

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

590

1180

1770

2360

2950

<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:

0.431

Hom.:

11669

Bravo

AF:

0.403

Asia WGS

AF:

0.409

AC:

1424

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

0.11

(source)

DANN

Benign

0.45

PhyloP100

-1.2

PromoterAI

-0.039

Neutral

(source)

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