chr22-36798672-A-C

Variant names:

• chr22-36798672-A-C
• rs4616572

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 0.93 in 152,190 control chromosomes in the GnomAD database, including 65,975 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 0.93 (65975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.973 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: 0.930 AC: 141458 AN: 152072 Hom.: 65922 Cov.: 32

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.929

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

GnomAD4 genome AF: 0.930 AC: 141566 AN: 152190 Hom.: 65975 Cov.: 32 AF XY: 0.928 AC XY: 69090 AN XY: 74416

African (AFR) AF: 0.981 AC: 40752 AN: 41522

American (AMR) AF: 0.868 AC: 13268 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3110 AN: 3470

East Asian (EAS) AF: 0.882 AC: 4549 AN: 5156

South Asian (SAS) AF: 0.833 AC: 4014 AN: 4816

European-Finnish (FIN) AF: 0.952 AC: 10105 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62667 AN: 68006

Other (OTH) AF: 0.928 AC: 1962 AN: 2114

Alfa AF: 0.922 Hom.: 21492

Bravo AF: 0.926

Asia WGS AF: 0.893 AC: 3106 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	1.5
DANN	Benign	0.34
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4616572; hg19: chr22-37194716;