chr9-84226487-C-T

Variant names:

• chr9-84226487-C-T
• rs10780656

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;