22-36800404-T-C

Variant names:

• chr22-36800404-T-C
• rs4821529

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 0.87 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.798 AC: 32821 AN: 41138

American (AMR) AF: 0.836 AC: 12736 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3048 AN: 3470

East Asian (EAS) AF: 0.886 AC: 4554 AN: 5138

South Asian (SAS) AF: 0.812 AC: 3890 AN: 4788

European-Finnish (FIN) AF: 0.939 AC: 9855 AN: 10492

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 61962 AN: 67976

Other (OTH) AF: 0.882 AC: 1853 AN: 2100

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs4821529; hg19: chr22-37196448;