rs17024019

Variant names:

• chr3-87208273-A-G
• rs17024019

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 0.0983 in 152,082 control chromosomes in the GnomAD database, including 776 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 0.098 (776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0983 AC: 14945 AN: 151962 Hom.: 775 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0829

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0983 AC: 14952 AN: 152082 Hom.: 776 Cov.: 32 AF XY: 0.0976 AC XY: 7257 AN XY: 74350

African (AFR) AF: 0.131 AC: 5414 AN: 41484

American (AMR) AF: 0.101 AC: 1540 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3468

East Asian (EAS) AF: 0.144 AC: 743 AN: 5172

South Asian (SAS) AF: 0.0770 AC: 371 AN: 4818

European-Finnish (FIN) AF: 0.0472 AC: 500 AN: 10600

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0829 AC: 5636 AN: 67964

Other (OTH) AF: 0.104 AC: 220 AN: 2108

Alfa AF: 0.0885 Hom.: 1291

Bravo AF: 0.106

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.33
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs17024019; hg19: chr3-87257423;