chr3-186781136-T-C

Variant names:

• chr3-186781136-T-C
• rs266714

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 0.835 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.822

Alfa AF: 0.806 Hom.: 10774

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs266714; hg19: chr3-186498925;