rs17300539

Variant names:

• chr3-186841671-G-A
• rs17300539

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 0.0532 in 152,198 control chromosomes in the GnomAD database, including 327 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 0.053 (327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0786 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: 0.0533 AC: 8099 AN: 152080 Hom.: 326 Cov.: 32

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.0756

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

GnomAD4 genome AF: 0.0532 AC: 8094 AN: 152198 Hom.: 327 Cov.: 32 AF XY: 0.0510 AC XY: 3792 AN XY: 74404

Gnomad4 AFR AF: 0.0146

Gnomad4 AMR AF: 0.0674

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0180

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0804

Gnomad4 OTH AF: 0.0748

Alfa AF: 0.0753 Hom.: 297

Bravo AF: 0.0567

Asia WGS AF: 0.0110 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17300539; hg19: chr3-186559460;