17-19538218-C-T

Position:

• chr17-19538218-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.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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC47A1	NM_018242.3	c.135+4144C>T		intron_variant		ENST00000270570.8	NP_060712.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC47A1	ENST00000270570.8	c.135+4144C>T		intron_variant		1	NM_018242.3	ENSP00000270570.4

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

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.333

Alfa AF: 0.337 Hom.: 12262

Bravo AF: 0.364

Asia WGS AF: 0.467 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.98
DANN	Benign	0.84

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: rs2018675; hg19: chr17-19441531;