rs2117985

Variant names:

• chr3-186835056-A-G
• rs2117985

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 0.0828 in 152,280 control chromosomes in the GnomAD database, including 889 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 0.083 (889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 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: 0.0828 AC: 12600 AN: 152162 Hom.: 886 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.0664

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0806

Gnomad OTH AF: 0.0732

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

GnomAD4 genome AF: 0.0828 AC: 12613 AN: 152280 Hom.: 889 Cov.: 32 AF XY: 0.0918 AC XY: 6839 AN XY: 74466

African (AFR) AF: 0.0168 AC: 700 AN: 41572

American (AMR) AF: 0.130 AC: 1993 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3472

East Asian (EAS) AF: 0.182 AC: 946 AN: 5186

South Asian (SAS) AF: 0.0663 AC: 320 AN: 4830

European-Finnish (FIN) AF: 0.252 AC: 2674 AN: 10596

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0806 AC: 5484 AN: 68018

Other (OTH) AF: 0.0753 AC: 159 AN: 2112

Alfa AF: 0.0857 Hom.: 78

Bravo AF: 0.0698

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.25
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs2117985; hg19: chr3-186552845;