17-19586483-A-G

Position:

• chr17-19586483-A-G

Variant summary

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

The variant allele was found at a frequency of 0.167 in 152,644 control chromosomes in the GnomAD database, including 2,538 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 0.17 (2533 hom., cov: 32)
  • Exomes 𝑓: 0.18 (5 hom.)
• Consequence: SLC47A1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

Genes affected

SLC47A1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC47A1P1		n.19586483A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290454	ENST00000420951.1	n.272+6148A>G		intron_variant		5
SLC47A1P1	ENST00000449666.3	n.348-141A>G		intron_variant		6
ENSG00000290454	ENST00000454535.5	n.130-3322A>G		intron_variant		2
ENSG00000262769	ENST00000574267.1	n.26+11414T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25337 AN: 152096 Hom.: 2534 Cov.: 32

Gnomad AFR AF: 0.0621

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.178

GnomAD4 exome AF: 0.179 AC: 77 AN: 430 Hom.: 5 AF XY: 0.185 AC XY: 47 AN XY: 254

Gnomad4 FIN exome AF: 0.182

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.167 AC: 25347 AN: 152214 Hom.: 2533 Cov.: 32 AF XY: 0.168 AC XY: 12474 AN XY: 74438

Gnomad4 AFR AF: 0.0620

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.179

Alfa AF: 0.190 Hom.: 1368

Bravo AF: 0.168

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2165894; hg19: chr17-19489796; COSMIC: COSV69510356;