3-186841685-C-G

Variant names:

• chr3-186841685-C-G
• rs266729

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 0.227 in 152,038 control chromosomes in the GnomAD database, including 4,383 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 0.23 (4383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 390 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 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: 0.227 AC: 34489 AN: 151920 Hom.: 4381 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.200

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.227 AC: 34523 AN: 152038 Hom.: 4383 Cov.: 32 AF XY: 0.230 AC XY: 17099 AN XY: 74310

African (AFR) AF: 0.125 AC: 5170 AN: 41486

American (AMR) AF: 0.250 AC: 3822 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3470

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5162

South Asian (SAS) AF: 0.269 AC: 1296 AN: 4812

European-Finnish (FIN) AF: 0.322 AC: 3399 AN: 10554

Middle Eastern (MID) AF: 0.208 AC: 60 AN: 288

European-Non Finnish (NFE) AF: 0.258 AC: 17556 AN: 67972

Other (OTH) AF: 0.218 AC: 459 AN: 2108

Alfa AF: 0.0979 Hom.: 179

Bravo AF: 0.221

Asia WGS AF: 0.273 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.93
DANN	Benign	0.69
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs266729; hg19: chr3-186559474;