rs2453583

Positions:

• chr17-19538723-A-T

Variant summary

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

The NM_018242.3(SLC47A1):​c.136-3670A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,074 control chromosomes in the GnomAD database, including 8,874 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 (8874 hom., cov: 32)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC47A1	NM_018242.3	c.136-3670A>T		intron_variant		ENST00000270570.8	NP_060712.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC47A1	ENST00000270570.8	c.136-3670A>T		intron_variant		1	NM_018242.3	ENSP00000270570.4

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50346 AN: 151956 Hom.: 8880 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.363

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.331 AC: 50357 AN: 152074 Hom.: 8874 Cov.: 32 AF XY: 0.321 AC XY: 23852 AN XY: 74364

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.363

Alfa AF: 0.353 Hom.: 1227

Bravo AF: 0.332

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.39
DANN	Benign	0.61

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: rs2453583; hg19: chr17-19442036;