17-19706634-C-G

Variant names:

• chr17-19706634-C-G
• rs12942065
• NM_001099646.3:c.841+14G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152908.5(SLC47A2):​c.949+14G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 1,565,744 control chromosomes in the GnomAD database, including 342,110 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 0.68 (35677 hom., cov: 33)
  • Exomes 𝑓: 0.66 (306433 hom.)
• Consequence: SLC47A2 NM_152908.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 11 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152908.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A2	NM_001099646.3	MANE Select	c.841+14G>C		intron	N/A	NP_001093116.1
	SLC47A2	NM_152908.5		c.949+14G>C		intron	N/A	NP_690872.2
	SLC47A2	NM_001256663.3		c.841+14G>C		intron	N/A	NP_001243592.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A2	ENST00000433844.4	TSL:5 MANE Select	c.841+14G>C		intron	N/A	ENSP00000391848.3
	SLC47A2	ENST00000325411.9	TSL:1	c.949+14G>C		intron	N/A	ENSP00000326671.5
	SLC47A2	ENST00000350657.9	TSL:1	c.841+14G>C		intron	N/A	ENSP00000338084.6

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103482 AN: 151916 Hom.: 35639 Cov.: 33

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.665

GnomAD2 exomes AF: 0.686 AC: 144734 AN: 210838 AF XY: 0.681

Gnomad AFR exome AF: 0.716

Gnomad AMR exome AF: 0.780

Gnomad ASJ exome AF: 0.595

Gnomad EAS exome AF: 0.950

Gnomad FIN exome AF: 0.574

Gnomad NFE exome AF: 0.642

Gnomad OTH exome AF: 0.651

GnomAD4 exome AF: 0.655 AC: 926081 AN: 1413710 Hom.: 306433 Cov.: 29 AF XY: 0.657 AC XY: 460957 AN XY: 701996

African (AFR) AF: 0.715 AC: 21699 AN: 30368

American (AMR) AF: 0.767 AC: 26550 AN: 34620

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 14389 AN: 24198

East Asian (EAS) AF: 0.953 AC: 34979 AN: 36690

South Asian (SAS) AF: 0.723 AC: 58220 AN: 80472

European-Finnish (FIN) AF: 0.584 AC: 30111 AN: 51566

Middle Eastern (MID) AF: 0.542 AC: 3024 AN: 5580

European-Non Finnish (NFE) AF: 0.640 AC: 699085 AN: 1091990

Other (OTH) AF: 0.653 AC: 38024 AN: 58226

GnomAD4 genome AF: 0.681 AC: 103577 AN: 152034 Hom.: 35677 Cov.: 33 AF XY: 0.682 AC XY: 50726 AN XY: 74324

African (AFR) AF: 0.718 AC: 29760 AN: 41432

American (AMR) AF: 0.734 AC: 11230 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2039 AN: 3470

East Asian (EAS) AF: 0.949 AC: 4893 AN: 5154

South Asian (SAS) AF: 0.741 AC: 3578 AN: 4830

European-Finnish (FIN) AF: 0.570 AC: 6023 AN: 10572

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43820 AN: 67966

Other (OTH) AF: 0.669 AC: 1414 AN: 2114

Alfa AF: 0.640 Hom.: 5609

Bravo AF: 0.690

Asia WGS AF: 0.851 AC: 2957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.31
PhyloP100		-2.1
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

Other links and lift over

dbSNP: rs12942065; hg19: chr17-19609947;