NM_018242.3:c.135+4144C>T

Variant names:

• chr17-19538218-C-T
• rs2018675
• NM_018242.3:c.135+4144C>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.135+4144C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,144 control chromosomes in the GnomAD database, including 10,272 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 0.36 (10272 hom., cov: 34)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 18 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 (EAS) allele frequency at 95% confidence interval = 0.542 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.135+4144C>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.135+4144C>T		intron	N/A	ENSP00000270570.4
	SLC47A1	ENST00000395585.5	TSL:1	c.135+4144C>T		intron	N/A	ENSP00000378951.1
	SLC47A1	ENST00000571335.5	TSL:1	c.-310-4175C>T		intron	N/A	ENSP00000462630.1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54704 AN: 152026 Hom.: 10261 Cov.: 34

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.360 AC: 54765 AN: 152144 Hom.: 10272 Cov.: 34 AF XY: 0.367 AC XY: 27285 AN XY: 74380

African (AFR) AF: 0.350 AC: 14511 AN: 41518

American (AMR) AF: 0.450 AC: 6886 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3470

East Asian (EAS) AF: 0.559 AC: 2891 AN: 5172

South Asian (SAS) AF: 0.379 AC: 1826 AN: 4818

European-Finnish (FIN) AF: 0.398 AC: 4207 AN: 10562

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22567 AN: 67992

Other (OTH) AF: 0.333 AC: 704 AN: 2114

Alfa AF: 0.341 Hom.: 19640

Bravo AF: 0.364

Asia WGS AF: 0.467 AC: 1622 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	0.98
DANN	Benign	0.84
PhyloP100		-0.41
Mutation Taster		=19/81	disease causing

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: rs2018675; hg19: chr17-19441531;