rs2823093

chr21-15148511-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 0.31 in 152,060 control chromosomes in the GnomAD database, including 7,959 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 0.31 (7959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 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: 0.309 AC: 47024 AN: 151942 Hom.: 7930 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.310 AC: 47107 AN: 152060 Hom.: 7959 Cov.: 32 AF XY: 0.308 AC XY: 22862 AN XY: 74318

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.0361

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.293

Alfa AF: 0.278 Hom.: 8787

Bravo AF: 0.320

Asia WGS AF: 0.191 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.9
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823093; hg19: chr21-16520832;