rs11013452

Variant names:

• chr10-23402678-G-A
• rs11013452

Your query was ambiguous. Multiple possible variants found:

• chr10-23402678-G-A
• chr10-23402678-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;