rs2828520

Variant names:

• chr21-23770802-G-A
• rs2828520

Your query was ambiguous. Multiple possible variants found:

• chr21-23770802-G-A
• chr21-23770802-G-C
• chr21-23770802-G-T

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 0.668 in 151,962 control chromosomes in the GnomAD database, including 34,271 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 0.67 (34271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101499 AN: 151844 Hom.: 34238 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.862

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.668 AC: 101575 AN: 151962 Hom.: 34271 Cov.: 32 AF XY: 0.675 AC XY: 50129 AN XY: 74266

African (AFR) AF: 0.595 AC: 24653 AN: 41426

American (AMR) AF: 0.729 AC: 11110 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2461 AN: 3470

East Asian (EAS) AF: 0.863 AC: 4436 AN: 5142

South Asian (SAS) AF: 0.688 AC: 3319 AN: 4826

European-Finnish (FIN) AF: 0.733 AC: 7741 AN: 10566

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45602 AN: 67968

Other (OTH) AF: 0.665 AC: 1401 AN: 2108

Alfa AF: 0.672 Hom.: 123232

Bravo AF: 0.667

Asia WGS AF: 0.758 AC: 2635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.35
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2828520; hg19: chr21-25143119;