rs10812426

Variant names:

• chr9-26609615-T-C
• rs10812426

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;