21-26833110-C-G

Variant names:

• chr21-26833110-C-G
• rs229038

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.895 in 152,260 control chromosomes in the GnomAD database, including 61,688 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 0.89 (61688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.953 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: 0.895 AC: 136123 AN: 152142 Hom.: 61629 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.895 AC: 136237 AN: 152260 Hom.: 61688 Cov.: 33 AF XY: 0.889 AC XY: 66153 AN XY: 74438

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.959

Gnomad4 OTH AF: 0.874

Alfa AF: 0.932 Hom.: 8223

Bravo AF: 0.892

Asia WGS AF: 0.711 AC: 2472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs229038; hg19: chr21-28205429;