21-26288563-A-C

Position:

• chr21-26288563-A-C

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 0.622 in 152,002 control chromosomes in the GnomAD database, including 29,990 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 (29990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94414 AN: 151884 Hom.: 29977 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.622 AC: 94474 AN: 152002 Hom.: 29990 Cov.: 32 AF XY: 0.625 AC XY: 46407 AN XY: 74270

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.649

Alfa AF: 0.660 Hom.: 44716

Bravo AF: 0.620

Asia WGS AF: 0.699 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs468345; hg19: chr21-27660882;