3-186835068-A-G

Variant names:

• chr3-186835068-A-G
• rs1656930

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 152,244 control chromosomes in the GnomAD database, including 56,332 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 (56332 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 6 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 = 0.864 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130801 AN: 152126 Hom.: 56288 Cov.: 33

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.871

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: 0.863

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

GnomAD4 genome AF: 0.860 AC: 130900 AN: 152244 Hom.: 56332 Cov.: 33 AF XY: 0.862 AC XY: 64158 AN XY: 74440

African (AFR) AF: 0.865 AC: 35931 AN: 41522

American (AMR) AF: 0.872 AC: 13335 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3045 AN: 3472

East Asian (EAS) AF: 0.885 AC: 4589 AN: 5186

South Asian (SAS) AF: 0.791 AC: 3817 AN: 4826

European-Finnish (FIN) AF: 0.918 AC: 9737 AN: 10606

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

European-Non Finnish (NFE) AF: 0.846 AC: 57550 AN: 68022

Other (OTH) AF: 0.864 AC: 1822 AN: 2108

Alfa AF: 0.856 Hom.: 11207

Bravo AF: 0.858

Asia WGS AF: 0.857 AC: 2980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.29
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1656930; hg19: chr3-186552857;