rs2829929

Variant names:

• chr21-25829998-C-T
• rs2829929

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.21 in 152,074 control chromosomes in the GnomAD database, including 3,705 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 0.21 (3705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 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: 0.210 AC: 31978 AN: 151956 Hom.: 3704 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.210 AC: 31986 AN: 152074 Hom.: 3705 Cov.: 32 AF XY: 0.210 AC XY: 15639 AN XY: 74340

African (AFR) AF: 0.154 AC: 6373 AN: 41506

American (AMR) AF: 0.145 AC: 2221 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3468

East Asian (EAS) AF: 0.124 AC: 642 AN: 5162

South Asian (SAS) AF: 0.318 AC: 1533 AN: 4814

European-Finnish (FIN) AF: 0.240 AC: 2536 AN: 10554

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17200 AN: 67980

Other (OTH) AF: 0.195 AC: 411 AN: 2106

Alfa AF: 0.247 Hom.: 2442

Bravo AF: 0.198

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.56
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2829929; hg19: chr21-27202309;