rs2206920

Variant names:

• chr20-6687532-G-A
• rs2206920

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0773 in 152,202 control chromosomes in the GnomAD database, including 532 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 0.077 (532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.117 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: 0.0772 AC: 11743 AN: 152084 Hom.: 531 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.0855

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.0798

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0773 AC: 11764 AN: 152202 Hom.: 532 Cov.: 32 AF XY: 0.0786 AC XY: 5852 AN XY: 74408

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0686

Gnomad4 EAS AF: 0.0859

Gnomad4 SAS AF: 0.0913

Gnomad4 FIN AF: 0.0798

Gnomad4 NFE AF: 0.0942

Gnomad4 OTH AF: 0.0715

Alfa AF: 0.0907 Hom.: 986

Bravo AF: 0.0767

Asia WGS AF: 0.0850 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Uncertain	24
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2206920; hg19: chr20-6668179;