17-19541674-A-G

Variant names:

• chr17-19541674-A-G
• rs2440154
• NM_018242.3:c.136-719A>G

Variant summary

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

The NM_018242.3(SLC47A1):​c.136-719A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 152,058 control chromosomes in the GnomAD database, including 36,450 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 0.69 (36450 hom., cov: 32)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530
• Publications: 10 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 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.136-719A>G		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.136-719A>G		intron	N/A	ENSP00000270570.4
	SLC47A1	ENST00000395585.5	TSL:1	c.136-719A>G		intron	N/A	ENSP00000378951.1
	SLC47A1	ENST00000571335.5	TSL:1	c.-310-719A>G		intron	N/A	ENSP00000462630.1

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104383 AN: 151940 Hom.: 36401 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.687 AC: 104486 AN: 152058 Hom.: 36450 Cov.: 32 AF XY: 0.689 AC XY: 51222 AN XY: 74322

African (AFR) AF: 0.780 AC: 32386 AN: 41500

American (AMR) AF: 0.710 AC: 10844 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2250 AN: 3466

East Asian (EAS) AF: 0.817 AC: 4218 AN: 5164

South Asian (SAS) AF: 0.744 AC: 3585 AN: 4818

European-Finnish (FIN) AF: 0.613 AC: 6472 AN: 10562

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42590 AN: 67952

Other (OTH) AF: 0.668 AC: 1411 AN: 2112

Alfa AF: 0.653 Hom.: 128397

Bravo AF: 0.698

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.61
PhyloP100		0.53
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: rs2440154; hg19: chr17-19444987;