9-84226487-C-T

Variant names:

• chr9-84226487-C-T
• rs10780656

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 0.72 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.719 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

African (AFR) AF: 0.913 AC: 37846 AN: 41460

American (AMR) AF: 0.755 AC: 11517 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2254 AN: 3466

East Asian (EAS) AF: 0.892 AC: 4601 AN: 5158

South Asian (SAS) AF: 0.811 AC: 3893 AN: 4798

European-Finnish (FIN) AF: 0.633 AC: 6648 AN: 10498

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40420 AN: 67928

Other (OTH) AF: 0.700 AC: 1473 AN: 2104

Alfa AF: 0.634 Hom.: 52567

Bravo AF: 0.736

Asia WGS AF: 0.866 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.38
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs10780656; hg19: chr9-86841402;