rs8065082

Positions:

• chr17-19561878-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018242.3(SLC47A1):​c.1106+1385C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,986 control chromosomes in the GnomAD database, including 14,536 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 0.43 (14536 hom., cov: 32)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

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]

SLC47A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC47A1	NM_018242.3	c.1106+1385C>T		intron_variant		ENST00000270570.8	NP_060712.2
LOC105371578	XR_934310.4	n.742-1353G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC47A1	ENST00000270570.8	c.1106+1385C>T		intron_variant		1	NM_018242.3	ENSP00000270570.4

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65561 AN: 151868 Hom.: 14543 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.431 AC: 65579 AN: 151986 Hom.: 14536 Cov.: 32 AF XY: 0.433 AC XY: 32173 AN XY: 74282

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.446

Alfa AF: 0.441 Hom.: 3612

Bravo AF: 0.436

Asia WGS AF: 0.527 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs8065082; hg19: chr17-19465191;