rs11013452

chr10-23402678-G-Achr10-23402678-G-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 0.106 in 152,216 control chromosomes in the GnomAD database, including 1,580 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 0.11 (1580 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16183 AN: 152098 Hom.: 1578 Cov.: 30

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0444

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.106 AC: 16203 AN: 152216 Hom.: 1580 Cov.: 30 AF XY: 0.109 AC XY: 8097 AN XY: 74424

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0951

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0541

Gnomad4 NFE AF: 0.0445

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0624 Hom.: 184

Bravo AF: 0.115

Asia WGS AF: 0.272 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.43
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11013452; hg19: chr10-23691607;