rs17429019

Variant names:

• chr3-189527356-A-G
• rs17429019

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 0.0628 in 152,256 control chromosomes in the GnomAD database, including 334 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 0.063 (334 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0887 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: 0.0629 AC: 9564 AN: 152138 Hom.: 334 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0467

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.0345

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0759

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

GnomAD4 genome AF: 0.0628 AC: 9566 AN: 152256 Hom.: 334 Cov.: 32 AF XY: 0.0612 AC XY: 4559 AN XY: 74470

African (AFR) AF: 0.0694 AC: 2885 AN: 41544

American (AMR) AF: 0.0633 AC: 968 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3468

East Asian (EAS) AF: 0.0467 AC: 242 AN: 5186

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4818

European-Finnish (FIN) AF: 0.0345 AC: 366 AN: 10608

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0591 AC: 4017 AN: 68018

Other (OTH) AF: 0.0747 AC: 158 AN: 2116

Alfa AF: 0.0634 Hom.: 51

Bravo AF: 0.0653

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.77
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs17429019; hg19: chr3-189245145;