rs9900497

Positions:

• chr17-19714080-G-T

Variant summary

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

The NM_001099646.3(SLC47A2):​c.295-107C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 1,434,550 control chromosomes in the GnomAD database, including 70,564 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 (8765 hom., cov: 33)
  • Exomes 𝑓: 0.31 (61799 hom.)
• Consequence: SLC47A2 NM_001099646.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.62

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC47A2	NM_001099646.3	c.295-107C>A		intron_variant		ENST00000433844.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC47A2	ENST00000433844.4	c.295-107C>A		intron_variant		5	NM_001099646.3	P1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50901 AN: 152024 Hom.: 8755 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.345

GnomAD4 exome AF: 0.306 AC: 392454 AN: 1282406 Hom.: 61799 AF XY: 0.309 AC XY: 192735 AN XY: 624328

Gnomad4 AFR exome AF: 0.337

Gnomad4 AMR exome AF: 0.339

Gnomad4 ASJ exome AF: 0.351

Gnomad4 EAS exome AF: 0.425

Gnomad4 SAS exome AF: 0.403

Gnomad4 FIN exome AF: 0.281

Gnomad4 NFE exome AF: 0.293

Gnomad4 OTH exome AF: 0.323

GnomAD4 genome AF: 0.335 AC: 50948 AN: 152144 Hom.: 8765 Cov.: 33 AF XY: 0.338 AC XY: 25143 AN XY: 74368

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.350

Alfa AF: 0.311 Hom.: 1594

Bravo AF: 0.339

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.096
DANN	Benign	0.88

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: rs9900497; hg19: chr17-19617393;