Variant chr1-111414903-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002557.4(OVGP1):c.1598C>G(p.Thr533Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 55 hom., cov: 16)

Exomes 𝑓: 0.0038 ( 65 hom. )

Consequence

OVGP1
NM_002557.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.163

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017255247).

BP6

Variant 1-111414903-G-C is Benign according to our data. Variant chr1-111414903-G-C is described in ClinVar as [Benign]. Clinvar id is 716048.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OVGP1	NM_002557.4 linkuse as main transcript	c.1598C>G	p.Thr533Ser	missense_variant	11/11	ENST00000369732.4
LOC124904309	XR_007066387.1 linkuse as main transcript	n.91+1G>C		splice_donor_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OVGP1	ENST00000369732.4 linkuse as main transcript	c.1598C>G	p.Thr533Ser	missense_variant	11/11	1	NM_002557.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0299

AC:

2308

AN:

77064

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00828

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000639

Gnomad OTH

AF:

0.0213

GnomAD3 exomes

AF:

0.00428

AC:

1054

AN:

246322

Hom.:

AF XY:

0.00318

AC XY:

424

AN XY:

133372

show subpopulations

Gnomad AFR exome

AF:

0.0632

Gnomad AMR exome

AF:

0.00249

Gnomad ASJ exome

AF:

0.000203

Gnomad EAS exome

AF:

0.0000546

Gnomad SAS exome

AF:

0.000200

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000365

Gnomad OTH exome

AF:

0.00232

GnomAD4 exome

AF:

0.00376

AC:

2562

AN:

681416

Hom.:

Cov.:

AF XY:

0.00329

AC XY:

1113

AN XY:

337948

show subpopulations

Gnomad4 AFR exome

AF:

0.128

Gnomad4 AMR exome

AF:

0.00508

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000160

Gnomad4 SAS exome

AF:

0.000357

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000653

Gnomad4 OTH exome

AF:

0.00728

GnomAD4 genome

AF:

0.0300

AC:

2310

AN:

77112

Hom.:

Cov.:

AF XY:

0.0288

AC XY:

1087

AN XY:

37714

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.00827

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000639

Gnomad4 OTH

AF:

0.0211

Alfa

AF:

0.00506

Hom.:

ESP6500AA

AF:

0.123

AC:

531

ESP6500EA

AF:

0.00978

AC:

ExAC

AF:

0.0103

AC:

622

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 13, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.092

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.014

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.042

LIST_S2

Benign

0.25

MetaRNN

Benign

0.0017

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.4

MutationTaster

Benign

1.0

PrimateAI

Benign

0.34

PROVEAN

Benign

-0.53

REVEL

Benign

0.059

Sift

Benign

0.046

Sift4G

Pathogenic

0.0

Polyphen

0.0050

Vest4

0.17

MutPred

0.19

Gain of sheet (P = 0.0016);

MPC

0.081

ClinPred

0.0015

GERP RS

-2.5

Varity_R

0.036

gMVP

0.068

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over