9-26609615-T-C

Variant names:

• chr9-26609615-T-C
• rs10812426

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 0.225 in 151,904 control chromosomes in the GnomAD database, including 3,918 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 0.22 (3918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34062 AN: 151786 Hom.: 3909 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.225 AC: 34105 AN: 151904 Hom.: 3918 Cov.: 32 AF XY: 0.227 AC XY: 16873 AN XY: 74236

African (AFR) AF: 0.280 AC: 11603 AN: 41442

American (AMR) AF: 0.175 AC: 2666 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3470

East Asian (EAS) AF: 0.192 AC: 987 AN: 5150

South Asian (SAS) AF: 0.170 AC: 818 AN: 4824

European-Finnish (FIN) AF: 0.276 AC: 2904 AN: 10516

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.203 AC: 13763 AN: 67940

Other (OTH) AF: 0.212 AC: 449 AN: 2114

Alfa AF: 0.203 Hom.: 5354

Bravo AF: 0.218

Asia WGS AF: 0.201 AC: 701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.37
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10812426; hg19: chr9-26609613;