9-90214308-G-T

Position:

• chr9-90214308-G-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 0.517 in 151,356 control chromosomes in the GnomAD database, including 21,570 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 0.52 (21570 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 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: 0.517 AC: 78156 AN: 151238 Hom.: 21530 Cov.: 29

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.517 AC: 78255 AN: 151356 Hom.: 21570 Cov.: 29 AF XY: 0.519 AC XY: 38343 AN XY: 73912

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.487

Alfa AF: 0.490 Hom.: 2634

Bravo AF: 0.517

Asia WGS AF: 0.672 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.64
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9775226; hg19: chr9-92976590;