9-90245759-C-T

Variant names:

• chr9-90245759-C-T
• rs10821091

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 0.442 in 151,984 control chromosomes in the GnomAD database, including 15,117 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 0.44 (15117 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 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: 0.442 AC: 67096 AN: 151866 Hom.: 15083 Cov.: 31

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.442 AC: 67190 AN: 151984 Hom.: 15117 Cov.: 31 AF XY: 0.447 AC XY: 33237 AN XY: 74312

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.454

Alfa AF: 0.413 Hom.: 16381

Bravo AF: 0.440

Asia WGS AF: 0.612 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10821091; hg19: chr9-93008041;