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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.650 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

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.725

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.583

Gnomad4 OTH AF: 0.669

Alfa AF: 0.590 Hom.: 11273

Bravo AF: 0.650

Asia WGS AF: 0.653 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2206917; hg19: chr20-6735511;