chr17-19706634-C-G

Position:

• chr17-19706634-C-G

Variant summary

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

The NM_001099646.3(SLC47A2):​c.841+14G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 1,565,744 control chromosomes in the GnomAD database, including 342,110 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 0.68 (35677 hom., cov: 33)
  • Exomes 𝑓: 0.66 (306433 hom.)
• Consequence: SLC47A2 NM_001099646.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC47A2	NM_001099646.3	c.841+14G>C		intron_variant		ENST00000433844.4	NP_001093116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC47A2	ENST00000433844.4	c.841+14G>C		intron_variant		5	NM_001099646.3	ENSP00000391848	P1

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103482 AN: 151916 Hom.: 35639 Cov.: 33

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.665

GnomAD3 exomes AF: 0.686 AC: 144734 AN: 210838 Hom.: 50766 AF XY: 0.681 AC XY: 78557 AN XY: 115286

Gnomad AFR exome AF: 0.716

Gnomad AMR exome AF: 0.780

Gnomad ASJ exome AF: 0.595

Gnomad EAS exome AF: 0.950

Gnomad SAS exome AF: 0.730

Gnomad FIN exome AF: 0.574

Gnomad NFE exome AF: 0.642

Gnomad OTH exome AF: 0.651

GnomAD4 exome AF: 0.655 AC: 926081 AN: 1413710 Hom.: 306433 Cov.: 29 AF XY: 0.657 AC XY: 460957 AN XY: 701996

Gnomad4 AFR exome AF: 0.715

Gnomad4 AMR exome AF: 0.767

Gnomad4 ASJ exome AF: 0.595

Gnomad4 EAS exome AF: 0.953

Gnomad4 SAS exome AF: 0.723

Gnomad4 FIN exome AF: 0.584

Gnomad4 NFE exome AF: 0.640

Gnomad4 OTH exome AF: 0.653

GnomAD4 genome AF: 0.681 AC: 103577 AN: 152034 Hom.: 35677 Cov.: 33 AF XY: 0.682 AC XY: 50726 AN XY: 74324

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.669

Alfa AF: 0.640 Hom.: 5609

Bravo AF: 0.690

Asia WGS AF: 0.851 AC: 2957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.31

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: rs12942065; hg19: chr17-19609947;