20-6786464-A-G

Variant names:

• chr20-6786464-A-G
• rs235756

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 0.378 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
• Publications: 28 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.441 AC: 18251 AN: 41410

American (AMR) AF: 0.357 AC: 5447 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1655 AN: 3458

East Asian (EAS) AF: 0.145 AC: 748 AN: 5172

South Asian (SAS) AF: 0.423 AC: 2037 AN: 4816

European-Finnish (FIN) AF: 0.376 AC: 3965 AN: 10532

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.354 AC: 24006 AN: 67890

Other (OTH) AF: 0.406 AC: 857 AN: 2110

Alfa AF: 0.360 Hom.: 19629

Bravo AF: 0.376

ClinVar

ClinVar submissions

Significance: confers sensitivity

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	-	Lung cancer (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.74
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs235756; hg19: chr20-6767111;