21-20539101-G-A

Variant names:

• chr21-20539101-G-A
• rs2826366

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 0.372 in 151,880 control chromosomes in the GnomAD database, including 10,546 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 0.37 (10546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56375 AN: 151762 Hom.: 10528 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.372 AC: 56458 AN: 151880 Hom.: 10546 Cov.: 32 AF XY: 0.377 AC XY: 27940 AN XY: 74206

African (AFR) AF: 0.341 AC: 14114 AN: 41416

American (AMR) AF: 0.404 AC: 6178 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1345 AN: 3464

East Asian (EAS) AF: 0.387 AC: 1994 AN: 5154

South Asian (SAS) AF: 0.473 AC: 2280 AN: 4822

European-Finnish (FIN) AF: 0.421 AC: 4425 AN: 10504

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 24974 AN: 67930

Other (OTH) AF: 0.365 AC: 769 AN: 2108

Alfa AF: 0.373 Hom.: 18625

Bravo AF: 0.365

Asia WGS AF: 0.437 AC: 1519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.39
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2826366; hg19: chr21-21911414;