Variant chr1-111414895-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_002557.4(OVGP1):c.1606A>G(p.Ser536Gly) 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 (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.011 ( 8 hom., cov: 0)

Exomes 𝑓: 0.0016 ( 15 hom. )

Consequence

OVGP1
NM_002557.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0760

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=0.0015309155).

BP6

Variant 1-111414895-T-C is Benign according to our data. Variant chr1-111414895-T-C is described in ClinVar as [Benign]. Clinvar id is 789431.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0108 (799/74254) while in subpopulation AFR AF= 0.0389 (728/18704). AF 95% confidence interval is 0.0366. There are 8 homozygotes in gnomad4. There are 366 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
OVGP1	NM_002557.4 link	c.1606A>G	p.Ser536Gly	missense_variant	11/11	ENST00000369732.4	NP_002548.3
LOC124904309	XR_007066387.1 link	n.84T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OVGP1	ENST00000369732.4 link	c.1606A>G	p.Ser536Gly	missense_variant	11/11	1	NM_002557.4	ENSP00000358747.3		Q12889

Frequencies

GnomAD3 genomes

AF:

0.0107

AC:

797

AN:

74222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0388

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00409

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00281

Gnomad SAS

AF:

0.000427

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000433

Gnomad OTH

AF:

0.0100

GnomAD3 exomes

AF:

0.00188

AC:

457

AN:

242878

Hom.:

AF XY:

0.00146

AC XY:

191

AN XY:

131182

show subpopulations

Gnomad AFR exome

AF:

0.0231

Gnomad AMR exome

AF:

0.00142

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00221

Gnomad SAS exome

AF:

0.000138

Gnomad FIN exome

AF:

0.0000481

Gnomad NFE exome

AF:

0.000127

Gnomad OTH exome

AF:

0.000674

GnomAD4 exome

AF:

0.00156

AC:

1047

AN:

670884

Hom.:

Cov.:

AF XY:

0.00140

AC XY:

464

AN XY:

332440

show subpopulations

Gnomad4 AFR exome

AF:

0.0502

Gnomad4 AMR exome

AF:

0.00241

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00218

Gnomad4 SAS exome

AF:

0.000674

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000290

Gnomad4 OTH exome

AF:

0.00451

GnomAD4 genome

AF:

0.0108

AC:

799

AN:

74254

Hom.:

Cov.:

AF XY:

0.0101

AC XY:

366

AN XY:

36288

show subpopulations

Gnomad4 AFR

AF:

0.0389

Gnomad4 AMR

AF:

0.00398

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00282

Gnomad4 SAS

AF:

0.000427

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000433

Gnomad4 OTH

AF:

0.00993

Alfa

AF:

0.296

Hom.:

3483

ESP6500AA

AF:

0.264

AC:

1138

ESP6500EA

AF:

0.284

AC:

2424

ExAC

AF:

0.00427

AC:

256

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	Jun 21, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.055

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.32

DANN

Benign

0.85

DEOGEN2

Benign

0.0037

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.019

LIST_S2

Benign

0.29

MetaRNN

Benign

0.0015

MetaSVM

Benign

-0.93

MutationAssessor

Benign

0.69

PrimateAI

Benign

0.30

PROVEAN

Benign

0.15

REVEL

Benign

0.030

Sift

Benign

0.19

Sift4G

Benign

0.20

Polyphen

0.0

Vest4

0.058

MVP

0.20

MPC

0.078

ClinPred

0.0015

GERP RS

-4.5

Varity_R

0.036

gMVP

0.059

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