20-6632185-A-G

Variant names:

• chr20-6632185-A-G
• rs1884897

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 0.626 in 151,964 control chromosomes in the GnomAD database, including 30,222 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 0.63 (30222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.33
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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: 0.626 AC: 94993 AN: 151846 Hom.: 30193 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.626 AC: 95071 AN: 151964 Hom.: 30222 Cov.: 32 AF XY: 0.629 AC XY: 46732 AN XY: 74262

African (AFR) AF: 0.540 AC: 22369 AN: 41444

American (AMR) AF: 0.726 AC: 11088 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1915 AN: 3464

East Asian (EAS) AF: 0.886 AC: 4566 AN: 5152

South Asian (SAS) AF: 0.563 AC: 2713 AN: 4816

European-Finnish (FIN) AF: 0.681 AC: 7189 AN: 10556

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43124 AN: 67940

Other (OTH) AF: 0.624 AC: 1315 AN: 2108

Alfa AF: 0.633 Hom.: 132021

Bravo AF: 0.628

Asia WGS AF: 0.691 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.7
DANN	Benign	0.67
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs1884897; hg19: chr20-6612832;