rs3834129

Variant names:

• chr2-201232808-TAGTAAG-T
• rs3834129

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 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

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 2-201232808-TAGTAAG-T is Benign according to our data. Variant chr2-201232808-TAGTAAG-T is described in ClinVar as [protective]. Clinvar id is 7763.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 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: 0.474 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

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.473

Alfa AF: 0.488 Hom.: 2221

Bravo AF: 0.476

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Significance: protective

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

Lung cancer, protection against Benign:1

Mar 01, 2008

OMIM

Significance: protective

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3834129; hg19: chr2-202097531;