rs4434089

chr22-23041683-A-Gchr22-23041683-A-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 0.62 in 152,156 control chromosomes in the GnomAD database, including 32,522 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 0.62 (32522 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

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 (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.620 AC: 94319 AN: 152038 Hom.: 32504 Cov.: 33

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.620 AC: 94370 AN: 152156 Hom.: 32522 Cov.: 33 AF XY: 0.630 AC XY: 46900 AN XY: 74390

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.990

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.709

Gnomad4 OTH AF: 0.664

Alfa AF: 0.681 Hom.: 12369

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	6.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4434089; hg19: chr22-23383863;