chr3-166043267-T-G

Variant names:

• chr3-166043267-T-G
• rs2034445

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 0.416 in 151,790 control chromosomes in the GnomAD database, including 13,493 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 0.42 (13493 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 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: 0.416 AC: 63072 AN: 151674 Hom.: 13477 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.416 AC: 63117 AN: 151790 Hom.: 13493 Cov.: 31 AF XY: 0.413 AC XY: 30655 AN XY: 74196

African (AFR) AF: 0.512 AC: 21188 AN: 41386

American (AMR) AF: 0.431 AC: 6569 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1451 AN: 3462

East Asian (EAS) AF: 0.240 AC: 1239 AN: 5162

South Asian (SAS) AF: 0.287 AC: 1384 AN: 4818

European-Finnish (FIN) AF: 0.360 AC: 3797 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.385 AC: 26135 AN: 67864

Other (OTH) AF: 0.425 AC: 893 AN: 2100

Alfa AF: 0.363 Hom.: 4864

Bravo AF: 0.426

Asia WGS AF: 0.313 AC: 1091 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.71
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs2034445; hg19: chr3-165761055; COSMIC: COSV50807692;