XM_047426878.1:c.*55T>C

Variant names:

• chr11-7687050-A-G
• rs7932813
• XM_047426878.1:c.*55T>C

Variant summary

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

The XM_047426878.1(OVCH2):​c.*55T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,818 control chromosomes in the GnomAD database, including 7,742 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 0.28 (7742 hom., cov: 31)
• Consequence: OVCH2 XM_047426878.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 15 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 = 0.521 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: 0.277 AC: 42008 AN: 151700 Hom.: 7736 Cov.: 31

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.277 AC: 42053 AN: 151818 Hom.: 7742 Cov.: 31 AF XY: 0.275 AC XY: 20395 AN XY: 74194

African (AFR) AF: 0.527 AC: 21784 AN: 41330

American (AMR) AF: 0.216 AC: 3294 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1026 AN: 5154

South Asian (SAS) AF: 0.143 AC: 690 AN: 4818

European-Finnish (FIN) AF: 0.197 AC: 2072 AN: 10512

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11839 AN: 67964

Other (OTH) AF: 0.272 AC: 572 AN: 2102

Alfa AF: 0.208 Hom.: 15176

Bravo AF: 0.295

Asia WGS AF: 0.187 AC: 651 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	4.4
DANN	Benign	0.52
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs7932813; hg19: chr11-7708281;