rs11041530

Variant names:

• chr11-7680272-G-C
• rs11041530
• XM_047426878.1:c.*332-1339C>G

Variant summary

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

The XR_007062576.1(LOC105376533):​n.48+3765G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0484 in 152,270 control chromosomes in the GnomAD database, including 341 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 0.048 (341 hom., cov: 33)
• Consequence: LOC105376533 XR_007062576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 5 publications found

Genes affected

OVCH2 (HGNC:29970): (ovochymase 2) Predicted to enable metal ion binding activity and serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LOC105376533 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0484 AC: 7361 AN: 152152 Hom.: 340 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0409

Gnomad FIN AF: 0.0203

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0123

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0484 AC: 7377 AN: 152270 Hom.: 341 Cov.: 33 AF XY: 0.0483 AC XY: 3593 AN XY: 74456

African (AFR) AF: 0.118 AC: 4888 AN: 41528

American (AMR) AF: 0.0547 AC: 837 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0521 AC: 181 AN: 3472

East Asian (EAS) AF: 0.0179 AC: 93 AN: 5184

South Asian (SAS) AF: 0.0408 AC: 197 AN: 4832

European-Finnish (FIN) AF: 0.0203 AC: 215 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0123 AC: 838 AN: 68028

Other (OTH) AF: 0.0511 AC: 108 AN: 2114

Alfa AF: 0.0323 Hom.: 20

Bravo AF: 0.0554

Asia WGS AF: 0.0320 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.6
DANN	Benign	0.65
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs11041530; hg19: chr11-7701503;