Genetic Variant SLC47A2:c.-130C>T (chr17-19716685-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000350657.9(SLC47A2):c.-130C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,342,742 control chromosomes in the GnomAD database, including 54,600 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 0.28 ( 6187 hom., cov: 33)

Exomes 𝑓: 0.28 ( 48413 hom. )

Consequence

SLC47A2
ENST00000350657.9 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0460

Publications

61 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:

LOC124903948 (HGNC:):

LOC124903948 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=-0.56).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC47A2	NM_001099646.3 link	c.-130C>T		upstream_gene_variant		ENST00000433844.4	NP_001093116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC47A2	ENST00000433844.4 link	c.-130C>T		upstream_gene_variant		5	NM_001099646.3	ENSP00000391848.3		Q86VL8-3C9JAE6

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

42248

AN:

152066

Hom.:

6180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.439

Gnomad SAS

AF:

0.380

Gnomad FIN

AF:

0.260

Gnomad MID

AF:

0.414

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.297

GnomAD4 exome

AF:

0.281

AC:

334297

AN:

1190558

Hom.:

48413

Cov.:

AF XY:

0.284

AC XY:

164445

AN XY:

578970

show subpopulations

African (AFR)

AF:

0.206

AC:

5378

AN:

26086

American (AMR)

AF:

0.347

AC:

5843

AN:

16838

Ashkenazi Jewish (ASJ)

AF:

0.340

AC:

6105

AN:

17976

East Asian (EAS)

AF:

0.383

AC:

12404

AN:

32370

South Asian (SAS)

AF:

0.396

AC:

22422

AN:

56642

European-Finnish (FIN)

AF:

0.263

AC:

9109

AN:

34570

Middle Eastern (MID)

AF:

0.363

AC:

1238

AN:

3412

European-Non Finnish (NFE)

AF:

0.270

AC:

257150

AN:

952786

Other (OTH)

AF:

0.294

AC:

14648

AN:

49878

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

11173

22346

33519

44692

55865

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9014

18028

27042

36056

45070

<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:

0.278

AC:

42278

AN:

152184

Hom.:

6187

Cov.:

AF XY:

0.282

AC XY:

20950

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.217

AC:

9031

AN:

41542

American (AMR)

AF:

0.347

AC:

5302

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.334

AC:

1160

AN:

3470

East Asian (EAS)

AF:

0.439

AC:

2271

AN:

5174

South Asian (SAS)

AF:

0.381

AC:

1835

AN:

4822

European-Finnish (FIN)

AF:

0.260

AC:

2749

AN:

10580

Middle Eastern (MID)

AF:

0.411

AC:

120

AN:

292

European-Non Finnish (NFE)

AF:

0.277

AC:

18842

AN:

67984

Other (OTH)

AF:

0.302

AC:

640

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1621

3242

4864

6485

8106

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

446

892

1338

1784

2230

<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:

0.283

Hom.:

8698

Bravo

AF:

0.279

Asia WGS

AF:

0.457

AC:

1589

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

8.7

(source)

DANN

Benign

0.75

PhyloP100

0.046

PromoterAI

0.19

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

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