NM_198185.7:c.1413+1363G>A

Variant names:

• chr11-7693695-C-T
• rs7924569
• NM_198185.7:c.1413+1363G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_198185.7(OVCH2):​c.1413+1363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0318 in 152,230 control chromosomes in the GnomAD database, including 176 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 0.032 (176 hom., cov: 33)
• Consequence: OVCH2 NM_198185.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 1 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OVCH2	NM_198185.7	c.1413+1363G>A		intron_variant	Intron 12 of 15	ENST00000533663.6	NP_937828.3
OVCH2	XM_047426878.1	c.1425+1363G>A		intron_variant	Intron 12 of 17		XP_047282834.1
LOC105376533	XR_007062576.1	n.953+1142C>T		intron_variant	Intron 4 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OVCH2	ENST00000533663.6	c.1413+1363G>A		intron_variant	Intron 12 of 15	5	NM_198185.7	ENSP00000484497.2
OVCH2	ENST00000612000.1	c.1413+1363G>A		intron_variant	Intron 12 of 14	5		ENSP00000484790.1
OVCH2	ENST00000673880.1	c.966+1363G>A		intron_variant	Intron 8 of 11			ENSP00000501258.1

Frequencies

GnomAD3 genomes AF: 0.0316 AC: 4808 AN: 152112 Hom.: 173 Cov.: 33

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0155

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0100

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0318 AC: 4836 AN: 152230 Hom.: 176 Cov.: 33 AF XY: 0.0303 AC XY: 2253 AN XY: 74448

African (AFR) AF: 0.0853 AC: 3542 AN: 41530

American (AMR) AF: 0.0154 AC: 235 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0401 AC: 139 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5188

South Asian (SAS) AF: 0.0294 AC: 142 AN: 4826

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10610

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0100 AC: 682 AN: 68000

Other (OTH) AF: 0.0284 AC: 60 AN: 2112

Alfa AF: 0.0364 Hom.: 78

Bravo AF: 0.0346

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	5.1
DANN	Benign	0.76
PhyloP100		-0.21
Mutation Taster		=100/0	polymorphism (auto)

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: rs7924569; hg19: chr11-7714926;