rs10466239

Variant names:

• chr10-43354379-C-T
• rs10466239
• ENST00000765039.1:n.111-3863G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000765039.1(ENSG00000285712):​n.111-3863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000285712 ENST00000765039.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671
• Publications: 7 publications found

Genes affected

ENSG00000285712 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000285712	ENST00000765039.1	n.111-3863G>A		intron_variant	Intron 1 of 2
ENSG00000285712	ENST00000765040.1	n.107-3239G>A		intron_variant	Intron 1 of 4
ENSG00000285712	ENST00000765041.1	n.96-3863G>A		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.0989 AC: 4100 AN: 41474

American (AMR) AF: 0.108 AC: 1645 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1066 AN: 5122

South Asian (SAS) AF: 0.104 AC: 499 AN: 4820

European-Finnish (FIN) AF: 0.169 AC: 1768 AN: 10492

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0774 AC: 5261 AN: 67936

Other (OTH) AF: 0.0829 AC: 175 AN: 2110

Alfa AF: 0.0811 Hom.: 111

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
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs10466239; hg19: chr10-43849827;