17-19555659-C-T

Variant names:

• chr17-19555659-C-T
• rs16960203
• NM_018242.3:c.708C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP7 BA1

The NM_018242.3(SLC47A1):​c.708C>T​(p.Leu236Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00569 in 1,614,214 control chromosomes in the GnomAD database, including 383 homozygotes. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.0089 (56 hom., cov: 32)
  • Exomes 𝑓: 0.0054 (327 hom.)
• Consequence: SLC47A1 NM_018242.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 6 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 -9 ACMG points.

• BP7: Synonymous conserved (PhyloP=-1.12 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0612 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.708C>T	p.Leu236Leu	synonymous	Exon 8 of 17	NP_060712.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC47A1	ENST00000270570.8	TSL:1 MANE Select	c.708C>T	p.Leu236Leu	synonymous	Exon 8 of 17	ENSP00000270570.4
	SLC47A1	ENST00000395585.5	TSL:1	c.708C>T	p.Leu236Leu	synonymous	Exon 8 of 19	ENSP00000378951.1
	SLC47A1	ENST00000571335.5	TSL:1	c.99-81C>T		intron	N/A	ENSP00000462630.1

Frequencies

GnomAD3 genomes AF: 0.00882 AC: 1343 AN: 152204 Hom.: 55 Cov.: 32

Gnomad AFR AF: 0.00287

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0538

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000353

Gnomad OTH AF: 0.0134

GnomAD2 exomes AF: 0.0180 AC: 4533 AN: 251478 AF XY: 0.0143

Gnomad AFR exome AF: 0.00228

Gnomad AMR exome AF: 0.0909

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0652

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000264

Gnomad OTH exome AF: 0.0147

GnomAD4 exome AF: 0.00536 AC: 7834 AN: 1461892 Hom.: 327 Cov.: 32 AF XY: 0.00483 AC XY: 3509 AN XY: 727246

African (AFR) AF: 0.00143 AC: 48 AN: 33480

American (AMR) AF: 0.0877 AC: 3922 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.0790 AC: 3136 AN: 39700

South Asian (SAS) AF: 0.00152 AC: 131 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53418

Middle Eastern (MID) AF: 0.000347 AC: 2 AN: 5768

European-Non Finnish (NFE) AF: 0.000154 AC: 171 AN: 1112012

Other (OTH) AF: 0.00702 AC: 424 AN: 60396

GnomAD4 genome AF: 0.00887 AC: 1351 AN: 152322 Hom.: 56 Cov.: 32 AF XY: 0.00992 AC XY: 739 AN XY: 74478

African (AFR) AF: 0.00286 AC: 119 AN: 41570

American (AMR) AF: 0.0542 AC: 830 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.0670 AC: 347 AN: 5182

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000353 AC: 24 AN: 68036

Other (OTH) AF: 0.0133 AC: 28 AN: 2112

Alfa AF: 0.00700 Hom.: 42

Bravo AF: 0.0131

Asia WGS AF: 0.0340 AC: 119 AN: 3478

EpiCase AF: 0.000218

EpiControl AF: 0.000296

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.0
DANN	Benign	0.73
PhyloP100		-1.1
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs16960203; hg19: chr17-19458972;