20-7646577-A-G

Variant names:

• chr20-7646577-A-G
• rs2050081

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 0.882 in 152,156 control chromosomes in the GnomAD database, including 59,396 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 0.88 (59396 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.882 AC: 134135 AN: 152038 Hom.: 59342 Cov.: 31

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.882 AC: 134246 AN: 152156 Hom.: 59396 Cov.: 31 AF XY: 0.885 AC XY: 65789 AN XY: 74372

African (AFR) AF: 0.903 AC: 37500 AN: 41518

American (AMR) AF: 0.911 AC: 13921 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2866 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5168 AN: 5170

South Asian (SAS) AF: 0.949 AC: 4568 AN: 4816

European-Finnish (FIN) AF: 0.840 AC: 8879 AN: 10566

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58464 AN: 68014

Other (OTH) AF: 0.873 AC: 1845 AN: 2114

Alfa AF: 0.867 Hom.: 46207

Bravo AF: 0.889

Asia WGS AF: 0.969 AC: 3371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs2050081; hg19: chr20-7627224;