21-22850940-T-C

Variant names:

• chr21-22850940-T-C
• rs243268

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 0.783 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.745 AC: 30899 AN: 41472

American (AMR) AF: 0.836 AC: 12765 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2791 AN: 3472

East Asian (EAS) AF: 0.860 AC: 4443 AN: 5164

South Asian (SAS) AF: 0.931 AC: 4491 AN: 4822

European-Finnish (FIN) AF: 0.763 AC: 8057 AN: 10564

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52872 AN: 67948

Other (OTH) AF: 0.794 AC: 1675 AN: 2110

Alfa AF: 0.782 Hom.: 58019

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
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs243268; hg19: chr21-24223261;