3-186836503-T-G

Variant names:

• chr3-186836503-T-G
• rs864265

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 0.86 in 151,974 control chromosomes in the GnomAD database, including 56,315 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 0.86 (56315 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 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: 0.860 AC: 130656 AN: 151856 Hom.: 56262 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.860 AC: 130766 AN: 151974 Hom.: 56315 Cov.: 30 AF XY: 0.863 AC XY: 64086 AN XY: 74294

African (AFR) AF: 0.868 AC: 35957 AN: 41448

American (AMR) AF: 0.872 AC: 13309 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3042 AN: 3470

East Asian (EAS) AF: 0.885 AC: 4576 AN: 5172

South Asian (SAS) AF: 0.791 AC: 3809 AN: 4816

European-Finnish (FIN) AF: 0.918 AC: 9689 AN: 10550

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57488 AN: 67942

Other (OTH) AF: 0.865 AC: 1824 AN: 2108

Alfa AF: 0.853 Hom.: 235481

Bravo AF: 0.858

Asia WGS AF: 0.857 AC: 2977 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.65
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs864265; hg19: chr3-186554292;