21-20448096-C-T

Variant names:

• chr21-20448096-C-T
• rs1735884

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 0.769 in 151,980 control chromosomes in the GnomAD database, including 45,093 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 0.77 (45093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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: 0.769 AC: 116760 AN: 151866 Hom.: 45083 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.769 AC: 116819 AN: 151980 Hom.: 45093 Cov.: 32 AF XY: 0.772 AC XY: 57318 AN XY: 74286

African (AFR) AF: 0.717 AC: 29650 AN: 41364

American (AMR) AF: 0.786 AC: 12003 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2823 AN: 3468

East Asian (EAS) AF: 0.888 AC: 4597 AN: 5174

South Asian (SAS) AF: 0.751 AC: 3623 AN: 4826

European-Finnish (FIN) AF: 0.812 AC: 8597 AN: 10582

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52984 AN: 67976

Other (OTH) AF: 0.770 AC: 1621 AN: 2106

Alfa AF: 0.771 Hom.: 97854

Bravo AF: 0.765

Asia WGS AF: 0.802 AC: 2788 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	0.37
DANN	Benign	0.19
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1735884; hg19: chr21-21820408;