Genetic Variant SLC47A2:p.Ala323Ala (chr17-19704119-C-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.969G>A(p.Ala323Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.031 in 1,612,154 control chromosomes in the GnomAD database, including 1,463 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 0.061 ( 537 hom., cov: 32)

Exomes 𝑓: 0.028 ( 926 hom. )

Consequence

SLC47A2
NM_001099646.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.987

Publications

8 publications found

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:

Genome browser will be placed here

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=-0.67).

BP7

Synonymous conserved (PhyloP=-0.987 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC47A2	NM_001099646.3 link	c.969G>A	p.Ala323Ala	synonymous_variant	Exon 11 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.969G>A	p.Ala323Ala	synonymous_variant	Exon 11 of 17	5	NM_001099646.3	ENSP00000391848.3		Q86VL8-3C9JAE6

Frequencies

GnomAD3 genomes

AF:

0.0607

AC:

9232

AN:

152134

Hom.:

537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0253

Gnomad ASJ

AF:

0.0225

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0273

Gnomad FIN

AF:

0.0334

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0257

Gnomad OTH

AF:

0.0508

GnomAD2 exomes

AF:

0.0315

AC:

7827

AN:

248300

AF XY:

0.0297

show subpopulations

Gnomad AFR exome

AF:

0.156

Gnomad AMR exome

AF:

0.0162

Gnomad ASJ exome

AF:

0.0245

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0333

Gnomad NFE exome

AF:

0.0254

Gnomad OTH exome

AF:

0.0320

GnomAD4 exome

AF:

0.0279

AC:

40660

AN:

1459902

Hom.:

926

Cov.:

AF XY:

0.0276

AC XY:

20031

AN XY:

726312

show subpopulations

African (AFR)

AF:

0.158

AC:

5264

AN:

33394

American (AMR)

AF:

0.0186

AC:

833

AN:

44682

Ashkenazi Jewish (ASJ)

AF:

0.0240

AC:

626

AN:

26106

East Asian (EAS)

AF:

0.0000504

AC:

AN:

39656

South Asian (SAS)

AF:

0.0256

AC:

2206

AN:

86148

European-Finnish (FIN)

AF:

0.0307

AC:

1597

AN:

52066

Middle Eastern (MID)

AF:

0.0442

AC:

255

AN:

5766

European-Non Finnish (NFE)

AF:

0.0251

AC:

27892

AN:

1111732

Other (OTH)

AF:

0.0329

AC:

1985

AN:

60352

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.466

Heterozygous variant carriers

1904

3809

5713

7618

9522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1100

2200

3300

4400

5500

<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:

0.0607

AC:

9247

AN:

152252

Hom.:

537

Cov.:

AF XY:

0.0598

AC XY:

4454

AN XY:

74462

show subpopulations

African (AFR)

AF:

0.155

AC:

6430

AN:

41526

American (AMR)

AF:

0.0252

AC:

386

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0225

AC:

AN:

3472

East Asian (EAS)

AF:

0.000579

AC:

AN:

5182

South Asian (SAS)

AF:

0.0271

AC:

131

AN:

4826

European-Finnish (FIN)

AF:

0.0334

AC:

354

AN:

10612

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0257

AC:

1751

AN:

68020

Other (OTH)

AF:

0.0498

AC:

105

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

415

830

1245

1660

2075

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<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:

0.0325

Hom.:

284

Bravo

AF:

0.0649

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.0251

EpiControl

AF:

0.0249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

5.7

(source)

DANN

Benign

0.78

PhyloP100

-0.99

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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