3-186836503-T-G

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 0.86 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.846

Gnomad4 OTH AF: 0.865

Alfa AF: 0.854 Hom.: 108485

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs864265; hg19: chr3-186554292;