rs3834129

chr2-201232808-TAGTAAG-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The variant allele was found at a frequency of 0.474 in 151,642 control chromosomes in the GnomAD database, including 17,450 homozygotes. 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

protective, no assertion criteria provided

literature only

OMIM

Mar 01, 2008

- -

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;