rs6022786

Variant names:

• chr20-53830764-A-G
• rs6022786

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 0.549 in 150,650 control chromosomes in the GnomAD database, including 23,136 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.55 (23136 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 26 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.624 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: 0.550 AC: 82724 AN: 150534 Hom.: 23129 Cov.: 29

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.549 AC: 82764 AN: 150650 Hom.: 23136 Cov.: 29 AF XY: 0.551 AC XY: 40432 AN XY: 73366

African (AFR) AF: 0.442 AC: 18142 AN: 41002

American (AMR) AF: 0.635 AC: 9549 AN: 15046

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1989 AN: 3466

East Asian (EAS) AF: 0.610 AC: 3133 AN: 5140

South Asian (SAS) AF: 0.512 AC: 2461 AN: 4806

European-Finnish (FIN) AF: 0.593 AC: 5930 AN: 9998

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39875 AN: 67898

Other (OTH) AF: 0.570 AC: 1192 AN: 2090

Alfa AF: 0.571 Hom.: 50891

Bravo AF: 0.549

Asia WGS AF: 0.511 AC: 1775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.014
DANN	Benign	0.49
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs6022786; hg19: chr20-52447303; COSMIC: COSV107192951;