17-19704119-C-T

Position:

• chr17-19704119-C-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.969G>A​(p.Ala323Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.031 in 1,612,154 control chromosomes in the GnomAD database, including 1,463 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 0.061 (537 hom., cov: 32)
  • Exomes 𝑓: 0.028 (926 hom.)
• Consequence: SLC47A2 NM_001099646.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BP7: Synonymous conserved (PhyloP=-0.987 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC47A2	NM_001099646.3	c.969G>A	p.Ala323Ala	synonymous_variant	11/17	ENST00000433844.4	NP_001093116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC47A2	ENST00000433844.4	c.969G>A	p.Ala323Ala	synonymous_variant	11/17	5	NM_001099646.3	ENSP00000391848.3

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9232 AN: 152134 Hom.: 537 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0253

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0273

Gnomad FIN AF: 0.0334

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0257

Gnomad OTH AF: 0.0508

GnomAD3 exomes AF: 0.0315 AC: 7827 AN: 248300 Hom.: 289 AF XY: 0.0297 AC XY: 3988 AN XY: 134476

Gnomad AFR exome AF: 0.156

Gnomad AMR exome AF: 0.0162

Gnomad ASJ exome AF: 0.0245

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0257

Gnomad FIN exome AF: 0.0333

Gnomad NFE exome AF: 0.0254

Gnomad OTH exome AF: 0.0320

GnomAD4 exome AF: 0.0279 AC: 40660 AN: 1459902 Hom.: 926 Cov.: 31 AF XY: 0.0276 AC XY: 20031 AN XY: 726312

Gnomad4 AFR exome AF: 0.158

Gnomad4 AMR exome AF: 0.0186

Gnomad4 ASJ exome AF: 0.0240

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.0256

Gnomad4 FIN exome AF: 0.0307

Gnomad4 NFE exome AF: 0.0251

Gnomad4 OTH exome AF: 0.0329

GnomAD4 genome AF: 0.0607 AC: 9247 AN: 152252 Hom.: 537 Cov.: 32 AF XY: 0.0598 AC XY: 4454 AN XY: 74462

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0252

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0271

Gnomad4 FIN AF: 0.0334

Gnomad4 NFE AF: 0.0257

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0380 Hom.: 160

Bravo AF: 0.0649

Asia WGS AF: 0.0180 AC: 63 AN: 3478

EpiCase AF: 0.0251

EpiControl AF: 0.0249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.7
DANN	Benign	0.78

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: rs34169093; hg19: chr17-19607432;