rs2826366

Positions:

• chr21-20539101-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;