9-84226487-C-T

Position:

• chr9-84226487-C-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 0.72 in 151,876 control chromosomes in the GnomAD database, including 40,772 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 0.72 (40772 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109166 AN: 151758 Hom.: 40697 Cov.: 30

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.720 AC: 109304 AN: 151876 Hom.: 40772 Cov.: 30 AF XY: 0.722 AC XY: 53600 AN XY: 74192

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.700

Alfa AF: 0.623 Hom.: 40301

Bravo AF: 0.736

Asia WGS AF: 0.866 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10780656; hg19: chr9-86841402;