11-7687050-A-G

Position:

• chr11-7687050-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OVCH2	XM_047426878.1	c.*55T>C		3_prime_UTR_variant	16/18		XP_047282834.1
		n.7687050A>G		intergenic_region
LOC105376533	XR_007062576.1	n.165+2822A>G		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.272

Alfa AF: 0.193 Hom.: 5626

Bravo AF: 0.295

Asia WGS AF: 0.187 AC: 651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7932813; hg19: chr11-7708281;