Genetic Variant SLC47A2:c.728-30G>A (chr17-19706791-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_001099646.3(SLC47A2):c.728-30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 1,556,340 control chromosomes in the GnomAD database, including 70,999 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 0.26 ( 5872 hom., cov: 33)

Exomes 𝑓: 0.30 ( 65127 hom. )

Consequence

SLC47A2
NM_001099646.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0150

Publications

11 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:

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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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099646.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC47A2	NM_001099646.3	MANE Select	c.728-30G>A	intron	N/A	NP_001093116.1	Q86VL8-3
SLC47A2	NM_152908.5		c.836-30G>A	intron	N/A	NP_690872.2
SLC47A2	NM_001256663.3		c.728-30G>A	intron	N/A	NP_001243592.1	Q86VL8-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC47A2	ENST00000433844.4	TSL:5 MANE Select	c.728-30G>A	intron	N/A	ENSP00000391848.3	Q86VL8-3
SLC47A2	ENST00000325411.9	TSL:1	c.836-30G>A	intron	N/A	ENSP00000326671.5	Q86VL8-1
SLC47A2	ENST00000350657.9	TSL:1	c.728-30G>A	intron	N/A	ENSP00000338084.6	Q86VL8-4

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38809

AN:

152034

Hom.:

5871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0994

Gnomad AMI

AF:

0.360

Gnomad AMR

AF:

0.330

Gnomad ASJ

AF:

0.334

Gnomad EAS

AF:

0.444

Gnomad SAS

AF:

0.398

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.297

Gnomad OTH

AF:

0.272

GnomAD2 exomes

AF:

0.323

AC:

72857

AN:

225514

AF XY:

0.331

show subpopulations

Gnomad AFR exome

AF:

0.0956

Gnomad AMR exome

AF:

0.362

Gnomad ASJ exome

AF:

0.331

Gnomad EAS exome

AF:

0.455

Gnomad FIN exome

AF:

0.294

Gnomad NFE exome

AF:

0.304

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.298

AC:

418252

AN:

1404188

Hom.:

65127

Cov.:

AF XY:

0.303

AC XY:

212594

AN XY:

701440

show subpopulations

African (AFR)

AF:

0.0873

AC:

2735

AN:

31334

American (AMR)

AF:

0.351

AC:

13523

AN:

38520

Ashkenazi Jewish (ASJ)

AF:

0.336

AC:

8423

AN:

25048

East Asian (EAS)

AF:

0.393

AC:

15193

AN:

38688

South Asian (SAS)

AF:

0.417

AC:

34619

AN:

83066

European-Finnish (FIN)

AF:

0.294

AC:

14582

AN:

49676

Middle Eastern (MID)

AF:

0.358

AC:

2014

AN:

5620

European-Non Finnish (NFE)

AF:

0.288

AC:

309737

AN:

1073878

Other (OTH)

AF:

0.299

AC:

17426

AN:

58358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

14101

28202

42302

56403

70504

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10154

20308

30462

40616

50770

<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:

0.255

AC:

38811

AN:

152152

Hom.:

5872

Cov.:

AF XY:

0.262

AC XY:

19459

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0993

AC:

4123

AN:

41522

American (AMR)

AF:

0.329

AC:

5030

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.334

AC:

1159

AN:

3472

East Asian (EAS)

AF:

0.444

AC:

2296

AN:

5170

South Asian (SAS)

AF:

0.398

AC:

1921

AN:

4826

European-Finnish (FIN)

AF:

0.292

AC:

3090

AN:

10588

Middle Eastern (MID)

AF:

0.388

AC:

114

AN:

294

European-Non Finnish (NFE)

AF:

0.297

AC:

20164

AN:

67972

Other (OTH)

AF:

0.278

AC:

586

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1436

2873

4309

5746

7182

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

418

836

1254

1672

2090

<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:

0.281

Hom.:

1170

Bravo

AF:

0.247

Asia WGS

AF:

0.458

AC:

1594

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.8

(source)

DANN

Benign

0.43

PhyloP100

-0.015

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