rs2209761

Variant names:

• chr20-6390364-C-T
• rs2209761

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 0.686 in 151,862 control chromosomes in the GnomAD database, including 36,238 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 0.69 (36238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 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: 0.686 AC: 104024 AN: 151744 Hom.: 36204 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.686 AC: 104114 AN: 151862 Hom.: 36238 Cov.: 32 AF XY: 0.687 AC XY: 51019 AN XY: 74248

African (AFR) AF: 0.784 AC: 32471 AN: 41428

American (AMR) AF: 0.717 AC: 10941 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2510 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4572 AN: 5152

South Asian (SAS) AF: 0.656 AC: 3157 AN: 4810

European-Finnish (FIN) AF: 0.656 AC: 6923 AN: 10556

Middle Eastern (MID) AF: 0.752 AC: 218 AN: 290

European-Non Finnish (NFE) AF: 0.609 AC: 41333 AN: 67878

Other (OTH) AF: 0.719 AC: 1519 AN: 2112

Alfa AF: 0.633 Hom.: 24952

Bravo AF: 0.700

Asia WGS AF: 0.757 AC: 2631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.73
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2209761; hg19: chr20-6371011;