rs11003134

Variant names:

• chr10-52778399-C-A
• rs11003134

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 0.134 in 152,206 control chromosomes in the GnomAD database, including 1,383 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 0.13 (1383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 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: 0.134 AC: 20429 AN: 152088 Hom.: 1382 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0902

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.134 AC: 20440 AN: 152206 Hom.: 1383 Cov.: 32 AF XY: 0.134 AC XY: 9998 AN XY: 74420

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.0895

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.145

Gnomad4 OTH AF: 0.145

Alfa AF: 0.143 Hom.: 2211

Bravo AF: 0.134

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.47
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11003134; hg19: chr10-54538159;