rs2829949

chr21-25850511-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 0.0452 in 152,220 control chromosomes in the GnomAD database, including 214 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 0.045 (214 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0728 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: 0.0453 AC: 6885 AN: 152102 Hom.: 214 Cov.: 33

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0308

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00724

Gnomad FIN AF: 0.0410

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0452 AC: 6882 AN: 152220 Hom.: 214 Cov.: 33 AF XY: 0.0426 AC XY: 3168 AN XY: 74414

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.0307

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00725

Gnomad4 FIN AF: 0.0410

Gnomad4 NFE AF: 0.0745

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0650 Hom.: 217

Bravo AF: 0.0438

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.023
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2829949; hg19: chr21-27222822;