rs428445

Variant names:

• chr20-56461491-C-A
• rs428445

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 0.627 in 151,992 control chromosomes in the GnomAD database, including 30,593 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 0.63 (30593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 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: 0.627 AC: 95196 AN: 151874 Hom.: 30561 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.627 AC: 95287 AN: 151992 Hom.: 30593 Cov.: 32 AF XY: 0.630 AC XY: 46836 AN XY: 74288

African (AFR) AF: 0.707 AC: 29322 AN: 41446

American (AMR) AF: 0.651 AC: 9937 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2460 AN: 3466

East Asian (EAS) AF: 0.942 AC: 4880 AN: 5178

South Asian (SAS) AF: 0.678 AC: 3267 AN: 4822

European-Finnish (FIN) AF: 0.551 AC: 5824 AN: 10564

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37469 AN: 67934

Other (OTH) AF: 0.646 AC: 1363 AN: 2110

Alfa AF: 0.578 Hom.: 12975

Bravo AF: 0.642

Asia WGS AF: 0.812 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.66
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs428445; hg19: chr20-55036547;