Genetic Variant 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: STRONG, MODERATE Submitted by: PanelApp Australia, 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_207113.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC37A3	NM_207113.3	MANE Select	c.882+10G>A	intron	N/A	NP_996996.1	Q8NCC5-1
SLC37A3	NM_001363373.1		c.882+10G>A	intron	N/A	NP_001350302.1
SLC37A3	NM_001287498.2		c.882+10G>A	intron	N/A	NP_001274427.1	Q8NCC5-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC37A3	ENST00000326232.14	TSL:1 MANE Select	c.882+10G>A	intron	N/A	ENSP00000321498.9	Q8NCC5-1
SLC37A3	ENST00000447932.6	TSL:1	c.882+10G>A	intron	N/A	ENSP00000397481.2	Q8NCC5-2
SLC37A3	ENST00000340308.7	TSL:1	c.882+10G>A	intron	N/A	ENSP00000343358.3	Q8NCC5-3

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over