22-32179227-A-G

Variant names:

• chr22-32179227-A-G
• rs136416

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 0.337 in 152,120 control chromosomes in the GnomAD database, including 9,677 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 0.34 (9677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51227 AN: 152002 Hom.: 9652 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.337 AC: 51299 AN: 152120 Hom.: 9677 Cov.: 32 AF XY: 0.333 AC XY: 24797 AN XY: 74376

African (AFR) AF: 0.501 AC: 20766 AN: 41452

American (AMR) AF: 0.211 AC: 3233 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 979 AN: 3472

East Asian (EAS) AF: 0.0906 AC: 470 AN: 5190

South Asian (SAS) AF: 0.289 AC: 1394 AN: 4826

European-Finnish (FIN) AF: 0.279 AC: 2954 AN: 10582

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20578 AN: 67990

Other (OTH) AF: 0.295 AC: 622 AN: 2106

Alfa AF: 0.328 Hom.: 1550

Bravo AF: 0.338

Asia WGS AF: 0.245 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.36
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs136416; hg19: chr22-32575214; COSMIC: COSV107150374;