rs2289669

Positions:

• chr17-19560030-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC47A1	NM_018242.3	c.922-158G>A		intron_variant		ENST00000270570.8	NP_060712.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC47A1	ENST00000270570.8	c.922-158G>A		intron_variant		1	NM_018242.3	ENSP00000270570	P1

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

Gnomad4 AFR exome AF: 0.0835

Gnomad4 AMR exome AF: 0.479

Gnomad4 ASJ exome AF: 0.506

Gnomad4 EAS exome AF: 0.445

Gnomad4 SAS exome AF: 0.502

Gnomad4 FIN exome AF: 0.364

Gnomad4 NFE exome AF: 0.411

Gnomad4 OTH exome AF: 0.413

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

Gnomad4 AFR AF: 0.0844

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.362

Alfa AF: 0.400 Hom.: 7037

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

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: rs2289669; hg19: chr17-19463343;