rs61733934

chr17-19534026-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BS1 BS2

The NM_018242.3(SLC47A1):c.87C>T(p.Ser29=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0122 in 1,547,452 control chromosomes in the GnomAD database, including 172 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 0.0096 (11 hom., cov: 32)
  • Exomes 𝑓: 0.013 (161 hom.)
• Consequence: SLC47A1 NM_018242.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP7: Synonymous conserved (PhyloP=-1.21 with no splicing effect.
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00964 (1469/152328) while in subpopulation SAS AF= 0.0234 (113/4832). AF 95% confidence interval is 0.0199. There are 11 homozygotes in gnomad4. There are 709 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC47A1	NM_018242.3	c.87C>T	p.Ser29=	synonymous_variant	1/17	ENST00000270570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC47A1	ENST00000270570.8	c.87C>T	p.Ser29=	synonymous_variant	1/17	1	NM_018242.3	P1

Frequencies

GnomAD3 genomes AF: 0.00966 AC: 1470 AN: 152212 Hom.: 11 Cov.: 32

Gnomad AFR AF: 0.00256

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0112

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.00518

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0125

Gnomad OTH AF: 0.0143

GnomAD3 exomes AF: 0.0131 AC: 1924 AN: 146932 Hom.: 25 AF XY: 0.0148 AC XY: 1172 AN XY: 79442

Gnomad AFR exome AF: 0.00192

Gnomad AMR exome AF: 0.00767

Gnomad ASJ exome AF: 0.0262

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0261

Gnomad FIN exome AF: 0.00412

Gnomad NFE exome AF: 0.0146

Gnomad OTH exome AF: 0.0155

GnomAD4 exome AF: 0.0125 AC: 17472 AN: 1395124 Hom.: 161 Cov.: 32 AF XY: 0.0133 AC XY: 9149 AN XY: 688936

Gnomad4 AFR exome AF: 0.00264

Gnomad4 AMR exome AF: 0.00872

Gnomad4 ASJ exome AF: 0.0244

Gnomad4 EAS exome AF: 0.000112

Gnomad4 SAS exome AF: 0.0257

Gnomad4 FIN exome AF: 0.00476

Gnomad4 NFE exome AF: 0.0124

Gnomad4 OTH exome AF: 0.0129

GnomAD4 genome AF: 0.00964 AC: 1469 AN: 152328 Hom.: 11 Cov.: 32 AF XY: 0.00952 AC XY: 709 AN XY: 74496

Gnomad4 AFR AF: 0.00255

Gnomad4 AMR AF: 0.0112

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0234

Gnomad4 FIN AF: 0.00518

Gnomad4 NFE AF: 0.0125

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.0133 Hom.: 9

Bravo AF: 0.00984

Asia WGS AF: 0.00867 AC: 30 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	7.9
Dann	Benign	0.92
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs61733934; hg19: chr17-19437339;