rs2826276

chr21-20463639-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.0288

Gnomad4 SAS AF: 0.0882

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.235

Alfa AF: 0.227 Hom.: 5200

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2826276; hg19: chr21-21835951;