rs2055109

Variant names:

• chr3-87418182-C-T
• rs2055109

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 0.809 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
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.873 AC: 36158 AN: 41440

American (AMR) AF: 0.836 AC: 12725 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2552 AN: 3468

East Asian (EAS) AF: 0.933 AC: 4808 AN: 5154

South Asian (SAS) AF: 0.821 AC: 3952 AN: 4814

European-Finnish (FIN) AF: 0.804 AC: 8419 AN: 10474

Middle Eastern (MID) AF: 0.799 AC: 230 AN: 288

European-Non Finnish (NFE) AF: 0.759 AC: 51550 AN: 67894

Other (OTH) AF: 0.791 AC: 1668 AN: 2110

Alfa AF: 0.774 Hom.: 73678

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2055109; hg19: chr3-87467332;