22-35379896-A-G

Position:

• chr22-35379896-A-G

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 0.613 in 151,496 control chromosomes in the GnomAD database, including 30,170 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 0.61 (30170 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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: 0.612 AC: 92702 AN: 151378 Hom.: 30136 Cov.: 28

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.613 AC: 92792 AN: 151496 Hom.: 30170 Cov.: 28 AF XY: 0.613 AC XY: 45369 AN XY: 73986

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.579

Alfa AF: 0.563 Hom.: 3006

Bravo AF: 0.613

Asia WGS AF: 0.710 AC: 2471 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	0.48
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3761439; hg19: chr22-35775889;