22-36267956-G-A

Variant names:

• chr22-36267956-G-A
• rs2012928

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 0.197 in 151,986 control chromosomes in the GnomAD database, including 3,192 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 0.20 (3192 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29821 AN: 151870 Hom.: 3182 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.197 AC: 29875 AN: 151986 Hom.: 3192 Cov.: 31 AF XY: 0.194 AC XY: 14430 AN XY: 74322

African (AFR) AF: 0.278 AC: 11527 AN: 41400

American (AMR) AF: 0.156 AC: 2387 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 463 AN: 3460

East Asian (EAS) AF: 0.0131 AC: 68 AN: 5182

South Asian (SAS) AF: 0.165 AC: 794 AN: 4812

European-Finnish (FIN) AF: 0.140 AC: 1482 AN: 10588

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12578 AN: 67950

Other (OTH) AF: 0.187 AC: 395 AN: 2112

Alfa AF: 0.184 Hom.: 5351

Bravo AF: 0.198

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2012928; hg19: chr22-36664002;