3-186781136-T-C

Variant names:

• chr3-186781136-T-C
• rs266714

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 0.835 in 152,252 control chromosomes in the GnomAD database, including 53,389 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 0.83 (53389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 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: 0.835 AC: 126973 AN: 152134 Hom.: 53328 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.835 AC: 127093 AN: 152252 Hom.: 53389 Cov.: 32 AF XY: 0.836 AC XY: 62234 AN XY: 74460

African (AFR) AF: 0.927 AC: 38510 AN: 41554

American (AMR) AF: 0.833 AC: 12752 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2657 AN: 3470

East Asian (EAS) AF: 0.905 AC: 4680 AN: 5172

South Asian (SAS) AF: 0.785 AC: 3780 AN: 4818

European-Finnish (FIN) AF: 0.842 AC: 8927 AN: 10608

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53076 AN: 68010

Other (OTH) AF: 0.822 AC: 1737 AN: 2114

Alfa AF: 0.806 Hom.: 12687

Bravo AF: 0.836

Asia WGS AF: 0.871 AC: 3028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.72
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs266714; hg19: chr3-186498925;