dbSNP rs10067: OVGP1:p.His604Gln (chr1-111414689-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002557.4(OVGP1):c.1812C>G(p.His604Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,613,860 control chromosomes in the GnomAD database, including 17,924 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.19 ( 4322 hom., cov: 32)

Exomes 𝑓: 0.11 ( 13602 hom. )

Consequence

OVGP1
NM_002557.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.531

Variant links:

Genes affected

OVGP1 (HGNC:8524): (oviductal glycoprotein 1) This gene encodes a large, carbohydrate-rich, epithelial glycoprotein with numerous O-glycosylation sites located within threonine, serine, and proline-rich tandem repeats. The gene is similar to members of the mucin and the glycosyl hydrolase 18 gene families. Regulation of expression may be estrogen-dependent. Gene expression and protein secretion occur during late follicular development through early cleavage-stage embryonic development. The protein is secreted from non-ciliated oviductal epithelial cells and associates with ovulated oocytes, blastomeres, and spermatozoan acrosomal regions. [provided by RefSeq, Jul 2008]

OVGP1 links:

LOC124904309 (HGNC:):

LOC124904309 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0015249252).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OVGP1	NM_002557.4 link	c.1812C>G	p.His604Gln	missense_variant	Exon 11 of 11	ENST00000369732.4	NP_002548.3
LOC124904309	XR_007066387.1 link	n.-123G>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OVGP1	ENST00000369732.4 link	c.1812C>G	p.His604Gln	missense_variant	Exon 11 of 11	1	NM_002557.4	ENSP00000358747.3		Q12889

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29450

AN:

151992

Hom.:

4313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.393

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.0894

Gnomad EAS

AF:

0.402

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0826

Gnomad OTH

AF:

0.186

GnomAD3 exomes

AF:

0.161

AC:

40335

AN:

251146

Hom.:

4692

AF XY:

0.157

AC XY:

21242

AN XY:

135732

show subpopulations

Gnomad AFR exome

AF:

0.406

Gnomad AMR exome

AF:

0.156

Gnomad ASJ exome

AF:

0.0889

Gnomad EAS exome

AF:

0.403

Gnomad SAS exome

AF:

0.219

Gnomad FIN exome

AF:

0.141

Gnomad NFE exome

AF:

0.0833

Gnomad OTH exome

AF:

0.132

GnomAD4 exome

AF:

0.109

AC:

159234

AN:

1461750

Hom.:

13602

Cov.:

AF XY:

0.111

AC XY:

80677

AN XY:

727174

show subpopulations

Gnomad4 AFR exome

AF:

0.409

Gnomad4 AMR exome

AF:

0.153

Gnomad4 ASJ exome

AF:

0.0893

Gnomad4 EAS exome

AF:

0.410

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.136

Gnomad4 NFE exome

AF:

0.0766

Gnomad4 OTH exome

AF:

0.132

GnomAD4 genome

AF:

0.194

AC:

29506

AN:

152110

Hom.:

4322

Cov.:

AF XY:

0.197

AC XY:

14655

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.393

Gnomad4 AMR

AF:

0.141

Gnomad4 ASJ

AF:

0.0894

Gnomad4 EAS

AF:

0.402

Gnomad4 SAS

AF:

0.232

Gnomad4 FIN

AF:

0.140

Gnomad4 NFE

AF:

0.0827

Gnomad4 OTH

AF:

0.184

Alfa

AF:

0.104

Hom.:

980

Bravo

AF:

0.205

TwinsUK

AF:

0.0758

AC:

281

ALSPAC

AF:

0.0771

AC:

297

ESP6500AA

AF:

0.386

AC:

1700

ESP6500EA

AF:

0.0824

AC:

709

ExAC

AF:

0.165

AC:

20004

Asia WGS

AF:

0.298

AC:

1036

AN:

3478

EpiCase

AF:

0.0879

EpiControl

AF:

0.0956

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.83

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.26

DANN

Benign

0.64

DEOGEN2

Benign

0.0073

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.036

LIST_S2

Benign

0.16

MetaRNN

Benign

0.0015

MetaSVM

Benign

-0.92

MutationAssessor

Benign

0.0

PrimateAI

Benign

0.24

PROVEAN

Benign

-0.34

REVEL

Benign

0.082

Sift

Benign

0.13

Sift4G

Benign

0.43

Polyphen

0.0050

Vest4

0.034

MutPred

0.051

Loss of catalytic residue at H604 (P = 0.0985);

MPC

0.089

ClinPred

0.0049

GERP RS

0.21

Varity_R

0.13

gMVP

0.045

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over