rs2826276

Variant names:

• chr21-20463639-A-G
• rs2826276

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 0.22 in 151,836 control chromosomes in the GnomAD database, including 3,966 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 0.22 (3966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 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: 0.220 AC: 33315 AN: 151720 Hom.: 3964 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.220 AC: 33338 AN: 151836 Hom.: 3966 Cov.: 32 AF XY: 0.212 AC XY: 15741 AN XY: 74200

African (AFR) AF: 0.251 AC: 10384 AN: 41382

American (AMR) AF: 0.222 AC: 3388 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 892 AN: 3464

East Asian (EAS) AF: 0.0288 AC: 149 AN: 5176

South Asian (SAS) AF: 0.0882 AC: 426 AN: 4832

European-Finnish (FIN) AF: 0.182 AC: 1922 AN: 10580

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15345 AN: 67844

Other (OTH) AF: 0.235 AC: 495 AN: 2104

Alfa AF: 0.228 Hom.: 6696

Bravo AF: 0.226

Asia WGS AF: 0.0930 AC: 323 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.34
DANN	Benign	0.70
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs2826276; hg19: chr21-21835951;