chr9-90245759-C-T

Variant names:

• chr9-90245759-C-T
• rs10821091

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.460 AC: 19088 AN: 41462

American (AMR) AF: 0.440 AC: 6722 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3472

East Asian (EAS) AF: 0.671 AC: 3463 AN: 5158

South Asian (SAS) AF: 0.539 AC: 2593 AN: 4808

European-Finnish (FIN) AF: 0.498 AC: 5264 AN: 10562

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27426 AN: 67944

Other (OTH) AF: 0.454 AC: 958 AN: 2110

Alfa AF: 0.415 Hom.: 20740

Bravo AF: 0.440

Asia WGS AF: 0.612 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.68
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs10821091; hg19: chr9-93008041;