rs10067

Variant names:

• chr1-111414689-G-C
• rs10067
• NM_002557.4:c.1812C>G
• OVGP1 p.His604Gln

Your query was ambiguous. Multiple possible variants found:

• chr1-111414689-G-C
• chr1-111414689-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.19 (4322 hom., cov: 32)
  • Exomes 𝑓: 0.11 (13602 hom.)
• Consequence: OVGP1 NM_002557.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 18 publications found

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]

LOC124904309 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002557.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OVGP1	NM_002557.4	MANE Select	c.1812C>G	p.His604Gln	missense	Exon 11 of 11	NP_002548.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OVGP1	ENST00000369732.4	TSL:1 MANE Select	c.1812C>G	p.His604Gln	missense	Exon 11 of 11	ENSP00000358747.3	Q12889
	OVGP1	ENST00000943842.1		c.1782C>G	p.His594Gln	missense	Exon 10 of 10	ENSP00000613901.1
	OVGP1	ENST00000943841.1		c.1626C>G	p.His542Gln	missense	Exon 10 of 10	ENSP00000613900.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29450 AN: 151992 Hom.: 4313 Cov.: 32

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

GnomAD2 exomes AF: 0.161 AC: 40335 AN: 251146 AF XY: 0.157

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 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.: 39 AF XY: 0.111 AC XY: 80677 AN XY: 727174

African (AFR) AF: 0.409 AC: 13682 AN: 33470

American (AMR) AF: 0.153 AC: 6853 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 2334 AN: 26130

East Asian (EAS) AF: 0.410 AC: 16279 AN: 39698

South Asian (SAS) AF: 0.218 AC: 18816 AN: 86250

European-Finnish (FIN) AF: 0.136 AC: 7257 AN: 53418

Middle Eastern (MID) AF: 0.154 AC: 887 AN: 5768

European-Non Finnish (NFE) AF: 0.0766 AC: 85149 AN: 1111902

Other (OTH) AF: 0.132 AC: 7977 AN: 60390

GnomAD4 genome AF: 0.194 AC: 29506 AN: 152110 Hom.: 4322 Cov.: 32 AF XY: 0.197 AC XY: 14655 AN XY: 74328

African (AFR) AF: 0.393 AC: 16303 AN: 41472

American (AMR) AF: 0.141 AC: 2164 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0894 AC: 310 AN: 3466

East Asian (EAS) AF: 0.402 AC: 2067 AN: 5148

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4820

European-Finnish (FIN) AF: 0.140 AC: 1485 AN: 10586

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0827 AC: 5622 AN: 68002

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.104 Hom.: 980

Bravo AF: 0.205

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 v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.83	T
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.26
DANN	Benign	0.64
DEOGEN2	Benign	0.0073	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.036	N
LIST_S2	Benign	0.16	T
MetaRNN	Benign	0.0015	T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.53
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-0.34	N
REVEL	Benign	0.082
Sift	Benign	0.13	T
Sift4G	Benign	0.43	T
Varity_R		0.13
gMVP		0.045
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10067;

hg19: chr1-111957311;

COSMIC: COSV63857932;

COSMIC: COSV63857932;