rs10466239

Positions:

• chr10-43354379-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;