rs12943590

chr17-19716685-G-A

Variant summary

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

The ENST00000350657.9(SLC47A2):c.-130C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,342,742 control chromosomes in the GnomAD database, including 54,600 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 0.28 (6187 hom., cov: 33)
  • Exomes 𝑓: 0.28 (48413 hom.)
• Consequence: SLC47A2 ENST00000350657.9 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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]

LOC124903948 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903948	XR_007065659.1	n.891-689G>A		intron_variant, non_coding_transcript_variant
SLC47A2	XM_017024222.3	c.-25+1426C>T		intron_variant
SLC47A2	NR_135624.2	n.869+1426C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC47A2	ENST00000350657.9	c.-130C>T		5_prime_UTR_variant	1/18	1
SLC47A2	ENST00000463318.5	n.869+1426C>T		intron_variant, non_coding_transcript_variant		1
SLC47A2	ENST00000456947.3	n.2153C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42248 AN: 152066 Hom.: 6180 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.297

GnomAD4 exome AF: 0.281 AC: 334297 AN: 1190558 Hom.: 48413 Cov.: 17 AF XY: 0.284 AC XY: 164445 AN XY: 578970

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.347

Gnomad4 ASJ exome AF: 0.340

Gnomad4 EAS exome AF: 0.383

Gnomad4 SAS exome AF: 0.396

Gnomad4 FIN exome AF: 0.263

Gnomad4 NFE exome AF: 0.270

Gnomad4 OTH exome AF: 0.294

GnomAD4 genome AF: 0.278 AC: 42278 AN: 152184 Hom.: 6187 Cov.: 33 AF XY: 0.282 AC XY: 20950 AN XY: 74402

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.302

Alfa AF: 0.267 Hom.: 1063

Bravo AF: 0.279

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	8.7
Dann	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12943590; hg19: chr17-19619998; COSMIC: COSV57627776; COSMIC: COSV57627776;