chr21-20265406-A-G

Variant names:

• chr21-20265406-A-G
• rs928862

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 0.148 in 152,158 control chromosomes in the GnomAD database, including 2,186 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 0.15 (2186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 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: 0.148 AC: 22529 AN: 152040 Hom.: 2181 Cov.: 32

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.148 AC: 22536 AN: 152158 Hom.: 2186 Cov.: 32 AF XY: 0.151 AC XY: 11258 AN XY: 74400

African (AFR) AF: 0.0380 AC: 1581 AN: 41566

American (AMR) AF: 0.229 AC: 3498 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1487 AN: 5174

South Asian (SAS) AF: 0.170 AC: 819 AN: 4826

European-Finnish (FIN) AF: 0.204 AC: 2154 AN: 10564

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12135 AN: 67972

Other (OTH) AF: 0.143 AC: 303 AN: 2112

Alfa AF: 0.161 Hom.: 3025

Bravo AF: 0.149

Asia WGS AF: 0.184 AC: 639 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.7
DANN	Benign	0.80
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs928862; hg19: chr21-21637719;