chr9-90270325-G-A

Position:

• chr9-90270325-G-A

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 0.225 in 152,108 control chromosomes in the GnomAD database, including 4,267 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 0.22 (4267 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.225 AC: 34190 AN: 151990 Hom.: 4266 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.225 AC: 34192 AN: 152108 Hom.: 4267 Cov.: 32 AF XY: 0.227 AC XY: 16893 AN XY: 74350

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.226

Alfa AF: 0.250 Hom.: 2930

Bravo AF: 0.210

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2798062; hg19: chr9-93032607;