rs2209981

Variant names:

• chr20-7012010-C-G
• rs2209981

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 0.777 in 152,152 control chromosomes in the GnomAD database, including 48,389 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 0.78 (48389 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 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: 0.777 AC: 118109 AN: 152036 Hom.: 48374 Cov.: 33

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.777 AC: 118154 AN: 152152 Hom.: 48389 Cov.: 33 AF XY: 0.776 AC XY: 57742 AN XY: 74384

African (AFR) AF: 0.491 AC: 20351 AN: 41464

American (AMR) AF: 0.858 AC: 13116 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3059 AN: 3468

East Asian (EAS) AF: 0.906 AC: 4690 AN: 5178

South Asian (SAS) AF: 0.862 AC: 4156 AN: 4820

European-Finnish (FIN) AF: 0.837 AC: 8863 AN: 10592

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61099 AN: 68026

Other (OTH) AF: 0.798 AC: 1685 AN: 2112

Alfa AF: 0.831 Hom.: 6716

Bravo AF: 0.767

Asia WGS AF: 0.856 AC: 2978 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2209981; hg19: chr20-6992657;