21-22455091-T-C

Variant names:

• chr21-22455091-T-C
• rs1542876

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 0.62 in 151,632 control chromosomes in the GnomAD database, including 29,403 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 (29403 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 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: 0.620 AC: 93934 AN: 151512 Hom.: 29389 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.620 AC: 93991 AN: 151632 Hom.: 29403 Cov.: 31 AF XY: 0.618 AC XY: 45789 AN XY: 74094

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.582

Alfa AF: 0.606 Hom.: 56397

Bravo AF: 0.606

Asia WGS AF: 0.510 AC: 1774 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	0.020
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: rs1542876; hg19: chr21-23827411;