22-35379896-A-G

Variant names:

• chr22-35379896-A-G
• rs3761439

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 0.613 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.845 AC: 34863 AN: 41276

American (AMR) AF: 0.448 AC: 6802 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1827 AN: 3466

East Asian (EAS) AF: 0.685 AC: 3527 AN: 5146

South Asian (SAS) AF: 0.646 AC: 3102 AN: 4800

European-Finnish (FIN) AF: 0.556 AC: 5817 AN: 10470

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35044 AN: 67858

Other (OTH) AF: 0.579 AC: 1221 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.48
DANN	Benign	0.11
PhyloP100		-0.44
PromoterAI		-0.016	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3761439; hg19: chr22-35775889;