17-19586483-A-G

Variant names:

• chr17-19586483-A-G
• rs2165894

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

SLC47A1P1 (HGNC:51849): (SLC47A1 pseudogene 1)

ENSG00000290454 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420951.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290454	ENST00000420951.1	TSL:5	n.272+6148A>G		intron	N/A
	SLC47A1P1	ENST00000449666.3	TSL:6	n.348-141A>G		intron	N/A
	ENSG00000290454	ENST00000454535.5	TSL:2	n.130-3322A>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.182 AC: 77 AN: 424

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.0620 AC: 2575 AN: 41554

American (AMR) AF: 0.253 AC: 3869 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3470

East Asian (EAS) AF: 0.357 AC: 1845 AN: 5174

South Asian (SAS) AF: 0.214 AC: 1034 AN: 4824

European-Finnish (FIN) AF: 0.173 AC: 1833 AN: 10602

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13274 AN: 67986

Other (OTH) AF: 0.179 AC: 377 AN: 2112

Alfa AF: 0.191 Hom.: 1541

Bravo AF: 0.168

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.2
DANN	Benign	0.77
PhyloP100		0.29

Splicing

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

Other links and lift over

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