20-7869280-A-G

Variant names:

• chr20-7869280-A-G
• rs2205824

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 0.335 in 152,126 control chromosomes in the GnomAD database, including 13,916 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 0.33 (13916 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 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: 0.334 AC: 50772 AN: 152008 Hom.: 13870 Cov.: 33

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.335 AC: 50890 AN: 152126 Hom.: 13916 Cov.: 33 AF XY: 0.333 AC XY: 24785 AN XY: 74370

African (AFR) AF: 0.730 AC: 30300 AN: 41492

American (AMR) AF: 0.316 AC: 4823 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2910 AN: 5160

South Asian (SAS) AF: 0.385 AC: 1853 AN: 4816

European-Finnish (FIN) AF: 0.0818 AC: 867 AN: 10604

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8642 AN: 67998

Other (OTH) AF: 0.322 AC: 680 AN: 2114

Alfa AF: 0.196 Hom.: 21237

Bravo AF: 0.369

Asia WGS AF: 0.503 AC: 1747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.76
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs2205824; hg19: chr20-7849927;