rs2206917

Variant names:

• chr20-6754864-G-A
• rs2206917

Your query was ambiguous. Multiple possible variants found:

• chr20-6754864-G-A
• chr20-6754864-G-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 0.65 in 152,016 control chromosomes in the GnomAD database, including 33,061 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 0.65 (33061 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98748 AN: 151898 Hom.: 33022 Cov.: 32

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.650 AC: 98832 AN: 152016 Hom.: 33061 Cov.: 32 AF XY: 0.648 AC XY: 48132 AN XY: 74298

African (AFR) AF: 0.810 AC: 33581 AN: 41482

American (AMR) AF: 0.542 AC: 8284 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2298 AN: 3472

East Asian (EAS) AF: 0.725 AC: 3739 AN: 5160

South Asian (SAS) AF: 0.581 AC: 2801 AN: 4818

European-Finnish (FIN) AF: 0.606 AC: 6382 AN: 10540

Middle Eastern (MID) AF: 0.743 AC: 217 AN: 292

European-Non Finnish (NFE) AF: 0.583 AC: 39597 AN: 67944

Other (OTH) AF: 0.669 AC: 1415 AN: 2114

Alfa AF: 0.593 Hom.: 22494

Bravo AF: 0.650

Asia WGS AF: 0.653 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.21
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2206917; hg19: chr20-6735511;