Genetic Variant SLC47A2:p.Gly115Gly (chr17-19713923-G-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001099646.3(SLC47A2):c.345C>A(p.Gly115Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,612,284 control chromosomes in the GnomAD database, including 80,909 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 0.33 ( 8272 hom., cov: 34)

Exomes 𝑓: 0.31 ( 72637 hom. )

Consequence

SLC47A2
NM_001099646.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.30

Variant links:

Genes affected

SLC47A2 (HGNC:26439): (solute carrier family 47 member 2) This gene encodes a protein belonging to a family of transporters involved in excretion of toxic electrolytes, both endogenous and exogenous, through urine and bile. This transporter family shares homology with the bacterial MATE (multidrug and toxin extrusion) protein family responsible for drug resistance. This gene is one of two members of the MATE transporter family located near each other on chromosome 17. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SLC47A2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP7

Synonymous conserved (PhyloP=-4.3 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC47A2	NM_001099646.3 link	c.345C>A	p.Gly115Gly	synonymous_variant	Exon 4 of 17	ENST00000433844.4	NP_001093116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC47A2	ENST00000433844.4 link	c.345C>A	p.Gly115Gly	synonymous_variant	Exon 4 of 17	5	NM_001099646.3	ENSP00000391848.3		Q86VL8-3C9JAE6

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49564

AN:

152002

Hom.:

8270

Cov.:

show subpopulations

Gnomad AFR

AF:

0.332

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.439

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.277

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.340

GnomAD2 exomes

AF:

0.345

AC:

86278

AN:

250102

AF XY:

0.348

show subpopulations

Gnomad AFR exome

AF:

0.335

Gnomad AMR exome

AF:

0.381

Gnomad ASJ exome

AF:

0.343

Gnomad EAS exome

AF:

0.450

Gnomad FIN exome

AF:

0.284

Gnomad NFE exome

AF:

0.310

Gnomad OTH exome

AF:

0.335

GnomAD4 exome

AF:

0.311

AC:

453692

AN:

1460164

Hom.:

72637

Cov.:

AF XY:

0.315

AC XY:

228686

AN XY:

726374

show subpopulations

Gnomad4 AFR exome

AF:

0.329

AC:

10988

AN:

33430

Gnomad4 AMR exome

AF:

0.377

AC:

16821

AN:

44600

Gnomad4 ASJ exome

AF:

0.347

AC:

9061

AN:

26076

Gnomad4 EAS exome

AF:

0.393

AC:

15576

AN:

39624

Gnomad4 SAS exome

AF:

0.420

AC:

36146

AN:

86036

Gnomad4 FIN exome

AF:

0.283

AC:

15055

AN:

53154

Gnomad4 NFE exome

AF:

0.296

AC:

328380

AN:

1111226

Gnomad4 Remaining exome

AF:

0.322

AC:

19415

AN:

60306

Heterozygous variant carriers

16378

32756

49135

65513

81891

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

10938

21876

32814

43752

54690

<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:

0.326

AC:

49596

AN:

152120

Hom.:

8272

Cov.:

AF XY:

0.329

AC XY:

24492

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.332

AC:

0.332298

AN:

0.332298

Gnomad4 AMR

AF:

0.366

AC:

0.365576

AN:

0.365576

Gnomad4 ASJ

AF:

0.344

AC:

0.344182

AN:

0.344182

Gnomad4 EAS

AF:

0.440

AC:

0.439705

AN:

0.439705

Gnomad4 SAS

AF:

0.401

AC:

0.401037

AN:

0.401037

Gnomad4 FIN

AF:

0.277

AC:

0.27675

AN:

0.27675

Gnomad4 NFE

AF:

0.305

AC:

0.304514

AN:

0.304514

Gnomad4 OTH

AF:

0.345

AC:

0.345351

AN:

0.345351

Heterozygous variant carriers

1749

3497

5246

6994

8743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

508

1016

1524

2032

2540

<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:

0.297

Hom.:

4688

Bravo

AF:

0.329

Asia WGS

AF:

0.475

AC:

1651

AN:

3478

EpiCase

AF:

0.325

EpiControl

AF:

0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.71

DANN

Benign

0.59

Mutation Taster

=100/0

polymorphism (auto)

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over