rs2826366

Variant names:

• chr21-20539101-G-A
• rs2826366

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 0.372 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.371 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

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.365

Alfa AF: 0.374 Hom.: 14870

Bravo AF: 0.365

Asia WGS AF: 0.437 AC: 1519 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2826366; hg19: chr21-21911414;