11-7691240-C-A

Variant names:

• chr11-7691240-C-A
• rs4509745
• NM_198185.7:c.1639+29G>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_198185.7(OVCH2):​c.1639+29G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: OVCH2 NM_198185.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 24 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: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OVCH2	NM_198185.7	c.1639+29G>T		intron_variant	Intron 14 of 15	ENST00000533663.6	NP_937828.3
OVCH2	XM_047426878.1	c.1651+29G>T		intron_variant	Intron 14 of 17		XP_047282834.1
LOC105376533	XR_007062576.1	n.166-38C>A		intron_variant	Intron 2 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OVCH2	ENST00000533663.6	c.1639+29G>T		intron_variant	Intron 14 of 15	5	NM_198185.7	ENSP00000484497.2
OVCH2	ENST00000612000.1	c.1639+29G>T		intron_variant	Intron 14 of 14	5		ENSP00000484790.1
OVCH2	ENST00000673880.1	c.1192+29G>T		intron_variant	Intron 10 of 11			ENSP00000501258.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 103109

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	3.1
DANN	Benign	0.82
PhyloP100		0.0010

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4509745; hg19: chr11-7712471;