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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.901

Alfa AF: 0.927 Hom.: 16192

Bravo AF: 0.881

Asia WGS AF: 0.899 AC: 3125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2209988; hg19: chr20-6968506;