22-36800404-T-C

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 0.87 in 151,544 control chromosomes in the GnomAD database, including 57,510 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 0.87 (57510 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.906 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: 0.870 AC: 131755 AN: 151426 Hom.: 57497 Cov.: 28

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.870 AC: 131813 AN: 151544 Hom.: 57510 Cov.: 28 AF XY: 0.870 AC XY: 64377 AN XY: 74028

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.939

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.882

Alfa AF: 0.896 Hom.: 12417

Bravo AF: 0.858

Asia WGS AF: 0.873 AC: 3034 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.96
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4821529; hg19: chr22-37196448;