chr22-35097374-C-A

Position:

• chr22-35097374-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.101 in 152,252 control chromosomes in the GnomAD database, including 2,403 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 0.10 (2403 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15262 AN: 152136 Hom.: 2391 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0357

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.0354

Gnomad FIN AF: 0.00960

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.00237

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.101 AC: 15319 AN: 152252 Hom.: 2403 Cov.: 33 AF XY: 0.0974 AC XY: 7252 AN XY: 74444

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.0401

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.00960

Gnomad4 NFE AF: 0.00237

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0169 Hom.: 302

Bravo AF: 0.112

Asia WGS AF: 0.0810 AC: 284 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5999715; hg19: chr22-35493367;