rs6022786

Variant names:

• chr20-53830764-A-G
• rs6022786

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 0.549 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.550 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

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.570

Alfa AF: 0.572 Hom.: 8980

Bravo AF: 0.549

Asia WGS AF: 0.511 AC: 1775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6022786; hg19: chr20-52447303;