rs2453583

Variant names:

• chr17-19538723-A-T
• rs2453583
• NM_018242.3:c.136-3670A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018242.3. 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
	SLC47A1	NM_018242.3	MANE Select	c.136-3670A>T		intron	N/A	NP_060712.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A1	ENST00000270570.8	TSL:1 MANE Select	c.136-3670A>T		intron	N/A	ENSP00000270570.4
	SLC47A1	ENST00000395585.5	TSL:1	c.136-3670A>T		intron	N/A	ENSP00000378951.1
	SLC47A1	ENST00000571335.5	TSL:1	c.-310-3670A>T		intron	N/A	ENSP00000462630.1

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

African (AFR) AF: 0.275 AC: 11394 AN: 41476

American (AMR) AF: 0.288 AC: 4392 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1542 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1115 AN: 5162

South Asian (SAS) AF: 0.193 AC: 929 AN: 4820

European-Finnish (FIN) AF: 0.269 AC: 2852 AN: 10592

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26909 AN: 67974

Other (OTH) AF: 0.363 AC: 765 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.39
DANN	Benign	0.61
PhyloP100		-0.93
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: rs2453583; hg19: chr17-19442036;