rs2206920

chr20-6687532-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;