chr17-19706791-C-T

Position:

• chr17-19706791-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC47A2	NM_001099646.3	c.728-30G>A		intron_variant		ENST00000433844.4	NP_001093116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC47A2	ENST00000433844.4	c.728-30G>A		intron_variant		5	NM_001099646.3	ENSP00000391848.3

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38809 AN: 152034 Hom.: 5871 Cov.: 33

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

GnomAD3 exomes AF: 0.323 AC: 72857 AN: 225514 Hom.: 12537 AF XY: 0.331 AC XY: 40833 AN XY: 123264

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 SAS exome AF: 0.419

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.: 23 AF XY: 0.303 AC XY: 212594 AN XY: 701440

Gnomad4 AFR exome AF: 0.0873

Gnomad4 AMR exome AF: 0.351

Gnomad4 ASJ exome AF: 0.336

Gnomad4 EAS exome AF: 0.393

Gnomad4 SAS exome AF: 0.417

Gnomad4 FIN exome AF: 0.294

Gnomad4 NFE exome AF: 0.288

Gnomad4 OTH exome AF: 0.299

GnomAD4 genome AF: 0.255 AC: 38811 AN: 152152 Hom.: 5872 Cov.: 33 AF XY: 0.262 AC XY: 19459 AN XY: 74382

Gnomad4 AFR AF: 0.0993

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.278

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.43

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: rs35263947; hg19: chr17-19610104; COSMIC: COSV57627027;