rs2244280

chr17-19556224-G-Achr17-19556224-G-C

Variant summary

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

The NM_018242.3(SLC47A1):c.921+162G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,224 control chromosomes in the GnomAD database, including 3,351 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 0.20 (3351 hom., cov: 32)
• Consequence: SLC47A1 NM_018242.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC47A1	NM_018242.3	c.921+162G>A		intron_variant		ENST00000270570.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC47A1	ENST00000270570.8	c.921+162G>A		intron_variant		1	NM_018242.3	P1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30976 AN: 152106 Hom.: 3343 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.204 AC: 31028 AN: 152224 Hom.: 3351 Cov.: 32 AF XY: 0.204 AC XY: 15206 AN XY: 74412

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.188

Alfa AF: 0.201 Hom.: 6799

Bravo AF: 0.198

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.6
Dann	Benign	0.55

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: rs2244280; hg19: chr17-19459537; COSMIC: COSV54501333; COSMIC: COSV54501333;