21-26804100-G-C

Variant names:

• chr21-26804100-G-C
• rs464903

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 0.619 in 151,956 control chromosomes in the GnomAD database, including 30,901 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 0.62 (30901 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.732 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: 0.619 AC: 94050 AN: 151838 Hom.: 30886 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.619 AC: 94101 AN: 151956 Hom.: 30901 Cov.: 32 AF XY: 0.618 AC XY: 45920 AN XY: 74264

African (AFR) AF: 0.447 AC: 18536 AN: 41430

American (AMR) AF: 0.575 AC: 8774 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2523 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1096 AN: 5144

South Asian (SAS) AF: 0.533 AC: 2567 AN: 4820

European-Finnish (FIN) AF: 0.794 AC: 8399 AN: 10584

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.738 AC: 50105 AN: 67936

Other (OTH) AF: 0.625 AC: 1319 AN: 2110

Alfa AF: 0.685 Hom.: 4563

Bravo AF: 0.595

Asia WGS AF: 0.403 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.70
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs464903; hg19: chr21-28176419;