Variant rs6111803 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_021220.4(OVOL2):c.327C>A(p.Thr109=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.064 in 1,610,476 control chromosomes in the GnomAD database, including 3,816 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.057 ( 286 hom., cov: 31)

Exomes 𝑓: 0.065 ( 3530 hom. )

Consequence

OVOL2
NM_021220.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.157

Variant links:

Genes affected

OVOL2 (HGNC:15804): (ovo like zinc finger 2) This gene encodes a member of the evolutionarily conserved ovo-like protein family. Mammalian members of this family contain a single zinc finger domain composed of a tetrad of C2H2 zinc fingers with variable N- and C-terminal extensions that contain intrinsically disordered domains. Members of this family are involved in epithelial development and differentiation. Knockout of this gene in mouse results in early embryonic lethality with phenotypes that include neurectoderm expansion, impaired vascularization, and heart anomalies. In humans, allelic variants of this gene have been associated with posterior polymorphous corneal dystrophy. [provided by RefSeq, Apr 2016]

OVOL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 20-18041718-G-T is Benign according to our data. Variant chr20-18041718-G-T is described in ClinVar as [Benign]. Clinvar id is 2037537.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.157 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
OVOL2	NM_021220.4 linkuse as main transcript	c.327C>A	p.Thr109=	synonymous_variant	3/4	ENST00000278780.7	NP_067043.2
OVOL2	NM_001303461.1 linkuse as main transcript	c.-70C>A		5_prime_UTR_variant	3/4		NP_001290390.1
OVOL2	NM_001303462.1 linkuse as main transcript	c.-70C>A		5_prime_UTR_variant	2/3		NP_001290391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
OVOL2	ENST00000278780.7 linkuse as main transcript	c.327C>A	p.Thr109=	synonymous_variant	3/4	1	NM_021220.4	ENSP00000278780	P1	Q9BRP0-1

Frequencies

GnomAD3 genomes

AF:

0.0570

AC:

8654

AN:

151878

Hom.:

286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0730

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0289

Gnomad ASJ

AF:

0.0210

Gnomad EAS

AF:

0.00482

Gnomad SAS

AF:

0.0353

Gnomad FIN

AF:

0.0240

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0671

Gnomad OTH

AF:

0.0465

GnomAD3 exomes

AF:

0.0435

AC:

10855

AN:

249776

Hom.:

323

AF XY:

0.0439

AC XY:

5929

AN XY:

135062

show subpopulations

Gnomad AFR exome

AF:

0.0707

Gnomad AMR exome

AF:

0.0191

Gnomad ASJ exome

AF:

0.0242

Gnomad EAS exome

AF:

0.00294

Gnomad SAS exome

AF:

0.0326

Gnomad FIN exome

AF:

0.0242

Gnomad NFE exome

AF:

0.0622

Gnomad OTH exome

AF:

0.0393

GnomAD4 exome

AF:

0.0647

AC:

94396

AN:

1458480

Hom.:

3530

Cov.:

AF XY:

0.0633

AC XY:

45879

AN XY:

725028

show subpopulations

Gnomad4 AFR exome

AF:

0.0699

Gnomad4 AMR exome

AF:

0.0212

Gnomad4 ASJ exome

AF:

0.0262

Gnomad4 EAS exome

AF:

0.00187

Gnomad4 SAS exome

AF:

0.0336

Gnomad4 FIN exome

AF:

0.0254

Gnomad4 NFE exome

AF:

0.0741

Gnomad4 OTH exome

AF:

0.0623

GnomAD4 genome

AF:

0.0570

AC:

8664

AN:

151996

Hom.:

286

Cov.:

AF XY:

0.0537

AC XY:

3993

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.0730

Gnomad4 AMR

AF:

0.0288

Gnomad4 ASJ

AF:

0.0210

Gnomad4 EAS

AF:

0.00483

Gnomad4 SAS

AF:

0.0355

Gnomad4 FIN

AF:

0.0240

Gnomad4 NFE

AF:

0.0671

Gnomad4 OTH

AF:

0.0460

Alfa

AF:

0.0602

Hom.:

411

Bravo

AF:

0.0581

Asia WGS

AF:

0.0290

AC:

101

AN:

3478

EpiCase

AF:

0.0629

EpiControl

AF:

0.0580

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 15, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

6.6

DANN

Benign

0.62

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