20-6786464-A-G

Variant names:

• chr20-6786464-A-G
• rs235756

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.378 in 151,868 control chromosomes in the GnomAD database, including 11,195 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as confers sensitivity (★).

• Frequency: Genomes: 𝑓 0.38 (11195 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: confers sensitivity criteria provided, single submitter O:1
• Conservation: PhyloP100: -0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 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: 0.378 AC: 57369 AN: 151750 Hom.: 11185 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.378 AC: 57399 AN: 151868 Hom.: 11195 Cov.: 32 AF XY: 0.379 AC XY: 28107 AN XY: 74226

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.406

Alfa AF: 0.356 Hom.: 11089

Bravo AF: 0.376

ClinVar

Significance: confers sensitivity

Submissions summary: Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

Lung cancer Other:1

May 01, 2012

Kong Lab, Department of Radiation Oncology, Case Western Reserve University School of Medicine

Significance: confers sensitivity

Review Status: criteria provided, single submitter

Collection Method: research

Improve the prediction accuracy for overal survival in non-small cell lung cancer patients -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs235756; hg19: chr20-6767111;