9-111102265-C-T

Variant names:

• chr9-111102265-C-T
• rs9299191

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 0.666 in 152,062 control chromosomes in the GnomAD database, including 34,138 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 0.67 (34138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101206 AN: 151944 Hom.: 34083 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.666 AC: 101318 AN: 152062 Hom.: 34138 Cov.: 32 AF XY: 0.670 AC XY: 49762 AN XY: 74318

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.662

Alfa AF: 0.616 Hom.: 48888

Bravo AF: 0.667

Asia WGS AF: 0.751 AC: 2610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.096
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9299191; hg19: chr9-113864545;