chr17-19703064-G-C

Variant names:

• chr17-19703064-G-C
• rs16960349
• NM_001099646.3:c.1094+28C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001099646.3(SLC47A2):​c.1094+28C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,604,252 control chromosomes in the GnomAD database, including 141 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 0.018 (72 hom., cov: 32)
  • Exomes 𝑓: 0.0020 (69 hom.)
• Consequence: SLC47A2 NM_001099646.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0597 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.1094+28C>G		intron	N/A	NP_001093116.1
	SLC47A2	NM_152908.5		c.1202+28C>G		intron	N/A	NP_690872.2
	SLC47A2	NM_001256663.3		c.1136+28C>G		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.1094+28C>G		intron	N/A	ENSP00000391848.3
	SLC47A2	ENST00000325411.9	TSL:1	c.1202+28C>G		intron	N/A	ENSP00000326671.5
	SLC47A2	ENST00000350657.9	TSL:1	c.1136+28C>G		intron	N/A	ENSP00000338084.6

Frequencies

GnomAD3 genomes AF: 0.0177 AC: 2695 AN: 152200 Hom.: 71 Cov.: 32

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00589

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000411

Gnomad OTH AF: 0.0134

GnomAD2 exomes AF: 0.00478 AC: 1199 AN: 250914 AF XY: 0.00362

Gnomad AFR exome AF: 0.0621

Gnomad AMR exome AF: 0.00348

Gnomad ASJ exome AF: 0.00139

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000432

Gnomad OTH exome AF: 0.00147

GnomAD4 exome AF: 0.00204 AC: 2958 AN: 1451934 Hom.: 69 Cov.: 29 AF XY: 0.00179 AC XY: 1294 AN XY: 722950

African (AFR) AF: 0.0646 AC: 2148 AN: 33274

American (AMR) AF: 0.00405 AC: 181 AN: 44690

Ashkenazi Jewish (ASJ) AF: 0.00142 AC: 37 AN: 26084

East Asian (EAS) AF: 0.00 AC: 0 AN: 39646

South Asian (SAS) AF: 0.000232 AC: 20 AN: 86026

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53328

Middle Eastern (MID) AF: 0.00261 AC: 15 AN: 5746

European-Non Finnish (NFE) AF: 0.000260 AC: 287 AN: 1103092

Other (OTH) AF: 0.00450 AC: 270 AN: 60048

GnomAD4 genome AF: 0.0178 AC: 2710 AN: 152318 Hom.: 72 Cov.: 32 AF XY: 0.0168 AC XY: 1253 AN XY: 74480

African (AFR) AF: 0.0616 AC: 2562 AN: 41560

American (AMR) AF: 0.00589 AC: 90 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000412 AC: 28 AN: 68040

Other (OTH) AF: 0.0132 AC: 28 AN: 2114

Alfa AF: 0.00995 Hom.: 9

Bravo AF: 0.0204

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.78
PhyloP100		0.0010
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs16960349; hg19: chr17-19606377;