chr2-201232808-TAGTAAG-T

Variant names:

• chr2-201232808-TAGTAAG-T
• rs3834129

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

Variant has been reported in ClinVar as protective (no stars).

• Frequency: Genomes: 𝑓 0.47 (17450 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: protective no assertion criteria provided B:1
• Conservation: PhyloP100: 0.642
• Publications: 146 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71774 AN: 151522 Hom.: 17436 Cov.: 0

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.474 AC: 71818 AN: 151642 Hom.: 17450 Cov.: 0 AF XY: 0.466 AC XY: 34518 AN XY: 74082

African (AFR) AF: 0.541 AC: 22380 AN: 41332

American (AMR) AF: 0.410 AC: 6253 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1518 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1091 AN: 5172

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4820

European-Finnish (FIN) AF: 0.480 AC: 5029 AN: 10474

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32842 AN: 67826

Other (OTH) AF: 0.473 AC: 1000 AN: 2112

Alfa AF: 0.488 Hom.: 2221

Bravo AF: 0.476

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: protective

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Lung cancer, protection against (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs3834129; hg19: chr2-202097531;