chr17-19714080-G-T

Variant names:

• chr17-19714080-G-T
• rs9900497
• NM_001099646.3:c.295-107C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099646.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A2	NM_001099646.3	MANE Select	c.295-107C>A		intron	N/A	NP_001093116.1
	SLC47A2	NM_152908.5		c.295-107C>A		intron	N/A	NP_690872.2
	SLC47A2	NM_001256663.3		c.295-107C>A		intron	N/A	NP_001243592.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A2	ENST00000433844.4	TSL:5 MANE Select	c.295-107C>A		intron	N/A	ENSP00000391848.3
	SLC47A2	ENST00000325411.9	TSL:1	c.295-107C>A		intron	N/A	ENSP00000326671.5
	SLC47A2	ENST00000350657.9	TSL:1	c.295-107C>A		intron	N/A	ENSP00000338084.6

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

African (AFR) AF: 0.337 AC: 9701 AN: 28748

American (AMR) AF: 0.339 AC: 8475 AN: 24968

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 6793 AN: 19376

East Asian (EAS) AF: 0.425 AC: 14854 AN: 34950

South Asian (SAS) AF: 0.403 AC: 25863 AN: 64222

European-Finnish (FIN) AF: 0.281 AC: 9696 AN: 34468

Middle Eastern (MID) AF: 0.408 AC: 1507 AN: 3690

European-Non Finnish (NFE) AF: 0.293 AC: 298414 AN: 1018872

Other (OTH) AF: 0.323 AC: 17151 AN: 53112

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

African (AFR) AF: 0.350 AC: 14510 AN: 41502

American (AMR) AF: 0.370 AC: 5659 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1239 AN: 3472

East Asian (EAS) AF: 0.487 AC: 2512 AN: 5162

South Asian (SAS) AF: 0.405 AC: 1953 AN: 4824

European-Finnish (FIN) AF: 0.288 AC: 3046 AN: 10594

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20816 AN: 67982

Other (OTH) AF: 0.350 AC: 739 AN: 2114

Alfa AF: 0.314 Hom.: 2195

Bravo AF: 0.339

Asia WGS AF: 0.494 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.096
DANN	Benign	0.88
PhyloP100		-4.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9900497; hg19: chr17-19617393;