22-35568675-C-T

Position:

• chr22-35568675-C-T

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 0.629 in 152,172 control chromosomes in the GnomAD database, including 30,831 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 0.63 (30831 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95712 AN: 152054 Hom.: 30830 Cov.: 34

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.629 AC: 95729 AN: 152172 Hom.: 30831 Cov.: 34 AF XY: 0.630 AC XY: 46859 AN XY: 74388

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.628

Alfa AF: 0.675 Hom.: 46547

Bravo AF: 0.613

Asia WGS AF: 0.529 AC: 1837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5750116; hg19: chr22-35964722;