20-24767796-A-G

Variant names:

• chr20-24767796-A-G
• rs2244284

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 0.542 in 152,000 control chromosomes in the GnomAD database, including 25,053 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 0.54 (25053 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 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: 0.542 AC: 82264 AN: 151880 Hom.: 24998 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.0205

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.542 AC: 82383 AN: 152000 Hom.: 25053 Cov.: 32 AF XY: 0.536 AC XY: 39794 AN XY: 74278

African (AFR) AF: 0.813 AC: 33759 AN: 41542

American (AMR) AF: 0.485 AC: 7400 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1847 AN: 3464

East Asian (EAS) AF: 0.0201 AC: 104 AN: 5162

South Asian (SAS) AF: 0.438 AC: 2100 AN: 4792

European-Finnish (FIN) AF: 0.444 AC: 4690 AN: 10554

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31001 AN: 67904

Other (OTH) AF: 0.494 AC: 1039 AN: 2104

Alfa AF: 0.500 Hom.: 7657

Bravo AF: 0.554

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.18
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2244284; hg19: chr20-24748432;