22-36797942-C-A

Variant names:

• chr22-36797942-C-A
• rs9610583

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 0.528 in 151,180 control chromosomes in the GnomAD database, including 25,110 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 0.53 (25110 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 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: 0.528 AC: 79737 AN: 151062 Hom.: 25102 Cov.: 29

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.528 AC: 79749 AN: 151180 Hom.: 25110 Cov.: 29 AF XY: 0.536 AC XY: 39550 AN XY: 73804

African (AFR) AF: 0.157 AC: 6501 AN: 41368

American (AMR) AF: 0.607 AC: 9239 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2579 AN: 3460

East Asian (EAS) AF: 0.699 AC: 3540 AN: 5068

South Asian (SAS) AF: 0.557 AC: 2648 AN: 4756

European-Finnish (FIN) AF: 0.725 AC: 7594 AN: 10478

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45491 AN: 67532

Other (OTH) AF: 0.615 AC: 1288 AN: 2096

Alfa AF: 0.621 Hom.: 65029

Bravo AF: 0.504

Asia WGS AF: 0.598 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.87
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs9610583; hg19: chr22-37193986;