21-23337880-A-G

Variant names:

• chr21-23337880-A-G
• rs2828074

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 0.452 in 151,980 control chromosomes in the GnomAD database, including 15,822 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 0.45 (15822 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68600 AN: 151862 Hom.: 15814 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.452 AC: 68657 AN: 151980 Hom.: 15822 Cov.: 32 AF XY: 0.446 AC XY: 33099 AN XY: 74286

African (AFR) AF: 0.415 AC: 17212 AN: 41450

American (AMR) AF: 0.486 AC: 7429 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1837 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1052 AN: 5170

South Asian (SAS) AF: 0.394 AC: 1896 AN: 4818

European-Finnish (FIN) AF: 0.414 AC: 4373 AN: 10558

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.492 AC: 33438 AN: 67924

Other (OTH) AF: 0.456 AC: 961 AN: 2108

Alfa AF: 0.484 Hom.: 75538

Bravo AF: 0.459

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.5
DANN	Benign	0.78
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs2828074; hg19: chr21-24710202;