rs17429019

chr3-189527356-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 0.0628 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0694

Gnomad4 AMR AF: 0.0633

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0467

Gnomad4 SAS AF: 0.0959

Gnomad4 FIN AF: 0.0345

Gnomad4 NFE AF: 0.0591

Gnomad4 OTH AF: 0.0747

Alfa AF: 0.0626 Hom.: 46

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17429019; hg19: chr3-189245145;