20-6987083-A-G

Variant names:

• chr20-6987083-A-G
• rs3885922

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 0.107 in 148,078 control chromosomes in the GnomAD database, including 1,378 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 0.11 (1378 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.294 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: 0.107 AC: 15859 AN: 147966 Hom.: 1370 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0344

Gnomad AMR AF: 0.0587

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0458

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.107 AC: 15893 AN: 148078 Hom.: 1378 Cov.: 31 AF XY: 0.107 AC XY: 7762 AN XY: 72408

African (AFR) AF: 0.225 AC: 8647 AN: 38486

American (AMR) AF: 0.0585 AC: 881 AN: 15070

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 581 AN: 3456

East Asian (EAS) AF: 0.306 AC: 1562 AN: 5102

South Asian (SAS) AF: 0.143 AC: 661 AN: 4636

European-Finnish (FIN) AF: 0.0162 AC: 170 AN: 10506

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0458 AC: 3093 AN: 67560

Other (OTH) AF: 0.111 AC: 229 AN: 2068

Alfa AF: 0.0698 Hom.: 1033

Bravo AF: 0.115

Asia WGS AF: 0.206 AC: 715 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.5
DANN	Benign	0.75
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs3885922; hg19: chr20-6967730;