rs2055109

chr3-87418182-C-T

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 0.809 in 151,774 control chromosomes in the GnomAD database, including 49,934 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 0.81 (49934 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.809 AC: 122704 AN: 151662 Hom.: 49881 Cov.: 29

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.800

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.809 AC: 122813 AN: 151774 Hom.: 49934 Cov.: 29 AF XY: 0.813 AC XY: 60320 AN XY: 74150

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.791

Alfa AF: 0.771 Hom.: 46864

Bravo AF: 0.814

Asia WGS AF: 0.870 AC: 3021 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	1.1
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2055109; hg19: chr3-87467332;