21-22941172-C-T

Variant names:

• chr21-22941172-C-T
• rs2827775

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 0.503 in 151,594 control chromosomes in the GnomAD database, including 19,206 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 0.50 (19206 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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 (SAS) allele frequency at 95% confidence interval = 0.569 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: 0.503 AC: 76214 AN: 151476 Hom.: 19183 Cov.: 31

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.503 AC: 76284 AN: 151594 Hom.: 19206 Cov.: 31 AF XY: 0.505 AC XY: 37369 AN XY: 74066

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.496

Alfa AF: 0.495 Hom.: 15892

Bravo AF: 0.505

Asia WGS AF: 0.505 AC: 1753 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2827775; hg19: chr21-24313493;