21-33391982-C-A

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 0.114 in 152,000 control chromosomes in the GnomAD database, including 1,513 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 0.11 (1513 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

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 (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17404 AN: 151882 Hom.: 1517 Cov.: 31

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.114 AC: 17394 AN: 152000 Hom.: 1513 Cov.: 31 AF XY: 0.120 AC XY: 8920 AN XY: 74280

Gnomad4 AFR AF: 0.0255

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.113

Alfa AF: 0.107 Hom.: 137

Bravo AF: 0.109

Asia WGS AF: 0.342 AC: 1186 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	1.8
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73194058; hg19: chr21-34764288;