chr9-90607502-A-G

Position:

• chr9-90607502-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 0.474 in 152,008 control chromosomes in the GnomAD database, including 17,155 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 0.47 (17155 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 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: 0.474 AC: 71975 AN: 151890 Hom.: 17146 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.474 AC: 72029 AN: 152008 Hom.: 17155 Cov.: 32 AF XY: 0.472 AC XY: 35080 AN XY: 74300

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.480

Alfa AF: 0.478 Hom.: 17876

Bravo AF: 0.476

Asia WGS AF: 0.384 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7868194; hg19: chr9-93369784;