NM_001099646.3:c.345C>A

Variant names:

• chr17-19713923-G-T
• rs4924792
• NM_001099646.3:c.345C>A

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.30
• Publications: 22 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 -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A2	NM_001099646.3	MANE Select	c.345C>A	p.Gly115Gly	synonymous	Exon 4 of 17	NP_001093116.1
	SLC47A2	NM_152908.5		c.345C>A	p.Gly115Gly	synonymous	Exon 4 of 17	NP_690872.2
	SLC47A2	NM_001256663.3		c.345C>A	p.Gly115Gly	synonymous	Exon 4 of 18	NP_001243592.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A2	ENST00000433844.4	TSL:5 MANE Select	c.345C>A	p.Gly115Gly	synonymous	Exon 4 of 17	ENSP00000391848.3
	SLC47A2	ENST00000325411.9	TSL:1	c.345C>A	p.Gly115Gly	synonymous	Exon 4 of 17	ENSP00000326671.5
	SLC47A2	ENST00000350657.9	TSL:1	c.345C>A	p.Gly115Gly	synonymous	Exon 4 of 18	ENSP00000338084.6

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49564 AN: 152002 Hom.: 8270 Cov.: 34

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

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.: 37 AF XY: 0.315 AC XY: 228686 AN XY: 726374

African (AFR) AF: 0.329 AC: 10988 AN: 33430

American (AMR) AF: 0.377 AC: 16821 AN: 44600

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 9061 AN: 26076

East Asian (EAS) AF: 0.393 AC: 15576 AN: 39624

South Asian (SAS) AF: 0.420 AC: 36146 AN: 86036

European-Finnish (FIN) AF: 0.283 AC: 15055 AN: 53154

Middle Eastern (MID) AF: 0.394 AC: 2250 AN: 5712

European-Non Finnish (NFE) AF: 0.296 AC: 328380 AN: 1111226

Other (OTH) AF: 0.322 AC: 19415 AN: 60306

GnomAD4 genome AF: 0.326 AC: 49596 AN: 152120 Hom.: 8272 Cov.: 34 AF XY: 0.329 AC XY: 24492 AN XY: 74360

African (AFR) AF: 0.332 AC: 13795 AN: 41514

American (AMR) AF: 0.366 AC: 5586 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1195 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2268 AN: 5158

South Asian (SAS) AF: 0.401 AC: 1933 AN: 4820

European-Finnish (FIN) AF: 0.277 AC: 2933 AN: 10598

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20696 AN: 67964

Other (OTH) AF: 0.345 AC: 728 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.71
DANN	Benign	0.59
PhyloP100		-4.3
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: rs4924792; hg19: chr17-19617236; COSMIC: COSV57626614; COSMIC: COSV57626614;