rs2383208

chr9-22132077-A-Gchr9-22132077-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 0.183 in 152,054 control chromosomes in the GnomAD database, including 2,764 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 0.18 (2764 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 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: 0.183 AC: 27758 AN: 151936 Hom.: 2760 Cov.: 30

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.183 AC: 27781 AN: 152054 Hom.: 2764 Cov.: 30 AF XY: 0.182 AC XY: 13558 AN XY: 74336

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.191

Alfa AF: 0.179 Hom.: 3625

Bravo AF: 0.187

Asia WGS AF: 0.293 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.4
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2383208; hg19: chr9-22132076;