17-19713923-G-T

Position:

• chr17-19713923-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001099646.3(SLC47A2):​c.345C>A​(p.Gly115=) 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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC47A2	NM_001099646.3	c.345C>A	p.Gly115=	synonymous_variant	4/17	ENST00000433844.4	NP_001093116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC47A2	ENST00000433844.4	c.345C>A	p.Gly115=	synonymous_variant	4/17	5	NM_001099646.3	ENSP00000391848	P1

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

GnomAD3 exomes AF: 0.345 AC: 86278 AN: 250102 Hom.: 15494 AF XY: 0.348 AC XY: 47157 AN XY: 135382

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 SAS exome AF: 0.421

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

Gnomad4 AFR exome AF: 0.329

Gnomad4 AMR exome AF: 0.377

Gnomad4 ASJ exome AF: 0.347

Gnomad4 EAS exome AF: 0.393

Gnomad4 SAS exome AF: 0.420

Gnomad4 FIN exome AF: 0.283

Gnomad4 NFE exome AF: 0.296

Gnomad4 OTH exome AF: 0.322

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

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.345

Alfa AF: 0.293 Hom.: 4091

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.71
DANN	Benign	0.59

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

LitVar

Other links and lift over

dbSNP: rs4924792; hg19: chr17-19617236; COSMIC: COSV57626614; COSMIC: COSV57626614;