chr21-22850940-T-C

Variant names:

• chr21-22850940-T-C
• rs243268

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 0.783 in 152,024 control chromosomes in the GnomAD database, including 46,645 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 0.78 (46645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.909 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: 0.783 AC: 118915 AN: 151906 Hom.: 46612 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.783 AC: 119002 AN: 152024 Hom.: 46645 Cov.: 32 AF XY: 0.787 AC XY: 58464 AN XY: 74322

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.931

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.794

Alfa AF: 0.783 Hom.: 44416

Bravo AF: 0.784

Asia WGS AF: 0.877 AC: 3045 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.84
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs243268; hg19: chr21-24223261;