rs10812426

chr9-26609615-T-C

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 0.225 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.224 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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.212

Alfa AF: 0.200 Hom.: 4055

Bravo AF: 0.218

Asia WGS AF: 0.201 AC: 701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.44
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10812426; hg19: chr9-26609613;