NM_018242.3:c.544-1016T>C

Variant names:

• chr17-19554196-T-C
• rs2453568
• NM_018242.3:c.544-1016T>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.544-1016T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,062 control chromosomes in the GnomAD database, including 39,330 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 0.71 (39330 hom., cov: 31)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 7 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A1	NM_018242.3	MANE Select	c.544-1016T>C		intron	N/A	NP_060712.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A1	ENST00000270570.8	TSL:1 MANE Select	c.544-1016T>C		intron	N/A	ENSP00000270570.4
	SLC47A1	ENST00000395585.5	TSL:1	c.544-1016T>C		intron	N/A	ENSP00000378951.1
	SLC47A1	ENST00000571335.5	TSL:1	c.99-1544T>C		intron	N/A	ENSP00000462630.1

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108534 AN: 151944 Hom.: 39285 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.714 AC: 108636 AN: 152062 Hom.: 39330 Cov.: 31 AF XY: 0.716 AC XY: 53184 AN XY: 74314

African (AFR) AF: 0.787 AC: 32663 AN: 41490

American (AMR) AF: 0.731 AC: 11164 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2695 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5154 AN: 5172

South Asian (SAS) AF: 0.719 AC: 3467 AN: 4822

European-Finnish (FIN) AF: 0.628 AC: 6632 AN: 10566

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44620 AN: 67958

Other (OTH) AF: 0.705 AC: 1488 AN: 2112

Alfa AF: 0.674 Hom.: 48888

Bravo AF: 0.728

Asia WGS AF: 0.867 AC: 3014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.38
PhyloP100		-0.76
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: rs2453568; hg19: chr17-19457509;