rs2209988

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;