rs2440155

Variant names:

• chr17-19543703-T-C
• rs2440155
• NM_018242.3:c.237+1209T>C

Variant summary

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

The NM_018242.3(SLC47A1):​c.237+1209T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,082 control chromosomes in the GnomAD database, including 2,769 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 0.19 (2769 hom., cov: 32)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 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.237+1209T>C		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.237+1209T>C		intron	N/A	ENSP00000270570.4
	SLC47A1	ENST00000395585.5	TSL:1	c.237+1209T>C		intron	N/A	ENSP00000378951.1
	SLC47A1	ENST00000571335.5	TSL:1	c.-209+1209T>C		intron	N/A	ENSP00000462630.1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28683 AN: 151964 Hom.: 2765 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.189 AC: 28723 AN: 152082 Hom.: 2769 Cov.: 32 AF XY: 0.190 AC XY: 14137 AN XY: 74330

African (AFR) AF: 0.190 AC: 7886 AN: 41492

American (AMR) AF: 0.159 AC: 2438 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1638 AN: 5158

South Asian (SAS) AF: 0.186 AC: 899 AN: 4822

European-Finnish (FIN) AF: 0.217 AC: 2294 AN: 10566

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12582 AN: 67972

Other (OTH) AF: 0.178 AC: 376 AN: 2110

Alfa AF: 0.183 Hom.: 10474

Bravo AF: 0.183

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.62
PhyloP100		-0.33
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: rs2440155; hg19: chr17-19447016;