rs2453580

Positions:

• chr17-19535008-T-C

Variant summary

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

The NM_018242.3(SLC47A1):​c.135+934T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,154 control chromosomes in the GnomAD database, including 10,740 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 0.37 (10716 hom., cov: 32)
  • Exomes 𝑓: 0.47 (24 hom.)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC47A1	NM_018242.3	c.135+934T>C		intron_variant		ENST00000270570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC47A1	ENST00000270570.8	c.135+934T>C		intron_variant		1	NM_018242.3	P1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55640 AN: 151850 Hom.: 10720 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.392

GnomAD4 exome AF: 0.468 AC: 87 AN: 186 Hom.: 24 Cov.: 0 AF XY: 0.458 AC XY: 65 AN XY: 142

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 SAS exome AF: 0.333

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.476

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.366 AC: 55670 AN: 151968 Hom.: 10716 Cov.: 32 AF XY: 0.355 AC XY: 26381 AN XY: 74274

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.392

Alfa AF: 0.400 Hom.: 18670

Bravo AF: 0.373

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.2
DANN	Benign	0.55

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: rs2453580; hg19: chr17-19438321;