20-6946722-A-G

Variant names:

• chr20-6946722-A-G
• rs6038661

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 0.85 in 152,222 control chromosomes in the GnomAD database, including 55,559 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 0.85 (55559 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129299 AN: 152104 Hom.: 55496 Cov.: 33

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.850 AC: 129424 AN: 152222 Hom.: 55559 Cov.: 33 AF XY: 0.847 AC XY: 63060 AN XY: 74422

African (AFR) AF: 0.908 AC: 37744 AN: 41564

American (AMR) AF: 0.868 AC: 13256 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2707 AN: 3472

East Asian (EAS) AF: 0.498 AC: 2574 AN: 5172

South Asian (SAS) AF: 0.698 AC: 3368 AN: 4828

European-Finnish (FIN) AF: 0.895 AC: 9502 AN: 10612

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57451 AN: 67980

Other (OTH) AF: 0.820 AC: 1733 AN: 2114

Alfa AF: 0.835 Hom.: 36108

Bravo AF: 0.853

Asia WGS AF: 0.648 AC: 2253 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs6038661; hg19: chr20-6927369;