rs2289669

Variant names:

• chr17-19560030-G-A
• rs2289669
• NM_018242.3:c.922-158G>A

Variant summary

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

The NM_018242.3(SLC47A1):​c.922-158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 596,556 control chromosomes in the GnomAD database, including 50,253 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 (10151 hom., cov: 31)
  • Exomes 𝑓: 0.42 (40102 hom.)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 112 publications found

Genes affected

SLC47A1 (HGNC:25588): (solute carrier family 47 member 1) This gene is located within the Smith-Magenis syndrome region on chromosome 17. It encodes a protein of unknown function. [provided by RefSeq, Jul 2008]

ENSG00000262769 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC47A1	NM_018242.3	c.922-158G>A		intron_variant	Intron 10 of 16	ENST00000270570.8	NP_060712.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC47A1	ENST00000270570.8	c.922-158G>A		intron_variant	Intron 10 of 16	1	NM_018242.3	ENSP00000270570.4

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49826 AN: 151828 Hom.: 10159 Cov.: 31

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.363

GnomAD4 exome AF: 0.416 AC: 185032 AN: 444610 Hom.: 40102 AF XY: 0.422 AC XY: 98895 AN XY: 234528

African (AFR) AF: 0.0835 AC: 1010 AN: 12102

American (AMR) AF: 0.479 AC: 8312 AN: 17366

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 6721 AN: 13270

East Asian (EAS) AF: 0.445 AC: 13231 AN: 29738

South Asian (SAS) AF: 0.502 AC: 22114 AN: 44034

European-Finnish (FIN) AF: 0.364 AC: 12088 AN: 33242

Middle Eastern (MID) AF: 0.563 AC: 1074 AN: 1906

European-Non Finnish (NFE) AF: 0.411 AC: 110073 AN: 267724

Other (OTH) AF: 0.413 AC: 10409 AN: 25228

GnomAD4 genome AF: 0.328 AC: 49814 AN: 151946 Hom.: 10151 Cov.: 31 AF XY: 0.333 AC XY: 24711 AN XY: 74252

African (AFR) AF: 0.0844 AC: 3501 AN: 41496

American (AMR) AF: 0.444 AC: 6770 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1789 AN: 3472

East Asian (EAS) AF: 0.491 AC: 2534 AN: 5158

South Asian (SAS) AF: 0.496 AC: 2380 AN: 4802

European-Finnish (FIN) AF: 0.357 AC: 3762 AN: 10530

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27866 AN: 67916

Other (OTH) AF: 0.362 AC: 764 AN: 2110

Alfa AF: 0.385 Hom.: 25325

Bravo AF: 0.324

Asia WGS AF: 0.484 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.60
DANN	Benign	0.51
PhyloP100		-0.38
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: rs2289669; hg19: chr17-19463343;