rs2209988

Variant names:

• chr20-6987859-A-G
• rs2209988

Your query was ambiguous. Multiple possible variants found:

• chr20-6987859-A-G
• chr20-6987859-A-T

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 0.889 in 152,098 control chromosomes in the GnomAD database, including 60,947 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 0.89 (60947 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572
• Publications: 0 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 (NFE) allele frequency at 95% confidence interval = 0.957 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: 0.889 AC: 135151 AN: 151980 Hom.: 60921 Cov.: 31

Gnomad AFR AF: 0.726

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.889 AC: 135224 AN: 152098 Hom.: 60947 Cov.: 31 AF XY: 0.889 AC XY: 66081 AN XY: 74338

African (AFR) AF: 0.726 AC: 30087 AN: 41452

American (AMR) AF: 0.932 AC: 14241 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.942 AC: 3269 AN: 3472

East Asian (EAS) AF: 0.889 AC: 4569 AN: 5142

South Asian (SAS) AF: 0.928 AC: 4477 AN: 4824

European-Finnish (FIN) AF: 0.941 AC: 9972 AN: 10596

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65528 AN: 68022

Other (OTH) AF: 0.901 AC: 1902 AN: 2110

Alfa AF: 0.930 Hom.: 136158

Bravo AF: 0.881

Asia WGS AF: 0.899 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.25
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2209988; hg19: chr20-6968506;