rs10466239

Variant names:

• chr10-43354379-C-T
• rs10466239

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 0.0967 in 151,874 control chromosomes in the GnomAD database, including 793 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 0.097 (793 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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: 0.0966 AC: 14667 AN: 151756 Hom.: 788 Cov.: 30

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0774

Gnomad OTH AF: 0.0824

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

GnomAD4 genome AF: 0.0967 AC: 14693 AN: 151874 Hom.: 793 Cov.: 30 AF XY: 0.102 AC XY: 7588 AN XY: 74214

Gnomad4 AFR AF: 0.0989

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.0774

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0802 Hom.: 109

Bravo AF: 0.0928

Asia WGS AF: 0.163 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10466239; hg19: chr10-43849827;