10-81513559-C-T

Variant names:

• chr10-81513559-C-T
• rs9332404

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 0.32 in 151,142 control chromosomes in the GnomAD database, including 8,260 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 0.32 (8260 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 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: 0.319 AC: 48245 AN: 151024 Hom.: 8250 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.320 AC: 48293 AN: 151142 Hom.: 8260 Cov.: 31 AF XY: 0.325 AC XY: 24018 AN XY: 73840

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.305

Alfa AF: 0.286 Hom.: 8256

Bravo AF: 0.316

Asia WGS AF: 0.524 AC: 1811 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332404; hg19: chr10-83273315;