rs2829803

Variant names:

• chr21-25575998-G-A
• rs2829803

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 0.589 in 151,934 control chromosomes in the GnomAD database, including 29,063 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 0.59 (29063 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 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: 0.590 AC: 89503 AN: 151816 Hom.: 29070 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.589 AC: 89503 AN: 151934 Hom.: 29063 Cov.: 31 AF XY: 0.580 AC XY: 43099 AN XY: 74246

African (AFR) AF: 0.361 AC: 14951 AN: 41390

American (AMR) AF: 0.544 AC: 8302 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2833 AN: 3468

East Asian (EAS) AF: 0.196 AC: 1012 AN: 5156

South Asian (SAS) AF: 0.437 AC: 2105 AN: 4818

European-Finnish (FIN) AF: 0.690 AC: 7268 AN: 10532

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50871 AN: 67982

Other (OTH) AF: 0.631 AC: 1331 AN: 2110

Alfa AF: 0.697 Hom.: 19473

Bravo AF: 0.572

Asia WGS AF: 0.309 AC: 1080 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6
DANN	Benign	0.67
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs2829803; hg19: chr21-26948310;