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MYOC
Final classification
VUS
MYOC c.719A>G · p.Glu240Gly
MYOC

NM_000261.2:c.719A>G (p.Glu240Gly) in MYOC is a rare missense variant absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (AF = 3.72e-06, 6/1,614,146 alleles), meeting PM2 at supporting strength per the ClinGen Glaucoma VCEP v2.1.

Gene
MYOC
Transcript
NM_000261.2
HGVS · transcript:coding
NM_000261.2:c.719A>G
Consequence
N/A
GRCh38
chr1:171638608 T>C
GRCh37
chr1:171607748 T>C
Basis ClinGen Glaucoma Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MYOC Version 2.1 v2.1 point-based framework: PM2 supporting (+1) + BP4 supporting (-1) = 0 points, which maps to VUS.
ClinGen Glaucoma Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MYOC Version 2.1 v2.1 point-based framework: PM2 supporting (+1) + BP4 supporting (-1) = 0 points, which maps to VUS.
Classification rationale
PM2 BP4 VUS
MYOC c.719A>G

NM_000261.2:c.719A>G (p.Glu240Gly) in MYOC is a rare missense variant absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (AF = 3.72e-06, 6/1,614,146 alleles), meeting PM2 at supporting strength per the ClinGen Glaucoma VCEP v2.1.1 The REVEL score of 0.205 falls within the VCEP BP4 supporting range (0.184-0.290), and SpliceAI predicts no splice impact (max delta = 0.01), meeting BP4 at supporting strength.2 This variant has been reported in ClinVar as Uncertain Significance by the ClinGen Glaucoma Variant Curation Expert Panel (ClinVar ID 2442275, reviewed by expert panel).3 No functional studies, de novo reports, proband counts, or segregation data were identified for this variant in the available literature. PS1, PS2, PS3, PS4, PP1, and BS3 remain not assessed due to absence of data. Under the Glaucoma VCEP v2.1 point-based scoring system, the variant accumulates +1 point (PM2_supporting) and -1 point (BP4_supporting), yielding a total of 0 points, which falls within the Uncertain Significance range (-1 to 5 points).4

PM2 + BP4 VUS
Gene diagram · NM_000261.2 · variants mapped to exon structure
MYOC NM_000261.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 10 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000261.2:c.719A>G is absent from gnomAD v2.1 and extremely rare in gnomAD v4.1 (AF = 3.72e-06, 6/1,614,146 alleles, 0 homozygotes; grpmax FAF = 1.83e-06). This meets the Glaucoma VCEP PM2 threshold of allele frequency ≤ 0.0001 (0.01%) at supporting strength.
gnomAD v2.1: variant absent.gnomAD v4.1: AF = 3.72e-06 (6/1614
BP4 supporting Benign
BP4 is met at supporting strength per the Glaucoma VCEP v2.1. The REVEL score for NM_000261.2:c.719A>G (p.Glu240Gly) is 0.205, falling within the supporting benign range of 0.184-0.290 for missense variants. Additionally, SpliceAI predicts no splice impact (max delta = 0.01, ≤0.1).
REVEL score = 0.205 (BP4_supporting range: 0.184-0.290 for missense variants).SpliceAI max delta = 0.01 (≤0.1no predicted splice impact).
Assessed · not applied
Pathogenic
PS1 No previously established pathogenic or likely pathogenic variant with the same amino acid change (p.Glu240Gly) has been reported.
PS2 No de novo reports were identified for NM_000261.2:c.719A>G (p.Glu240Gly) in the literature.
PS3 No functional assay data (solubility, secretion, or aggregation assays with OddsPath calculations) were identified for NM_000261.2:c.719A>G (p.Glu240Gly) in the literature.
PS4 No proband counts from independent studies were identified for NM_000261.2:c.719A>G (p.Glu240Gly).
PM5 PM5 is not met for NM_000261.2:c.719A>G (p.Glu240Gly).
PP1 No co-segregation data were identified for NM_000261.2:c.719A>G (p.Glu240Gly).
PP3 PP3 is not met for NM_000261.2:c.719A>G (p.Glu240Gly).
Benign
BA1 BA1 is not met.
BS1 BS1 is not met.
BS3 No functional assay data demonstrating normal solubility or secretion were identified for NM_000261.2:c.719A>G (p.Glu240Gly).
N/A · 13 PVS1 · PM1 · PM6 · PP2 · PP4 · PP5 · BS2 · BS4 · BP1 · BP2 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 3.71714e-06; MAF= 0.00037%, 6/1614146 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.08472e-06; MAF= 0.00051%, 6/1180006 alleles, homozygotes = 0); grpmax FAF= 1.83e-06.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00037% · 6 / 1,614,146
0 hom · FAF 0.00018%
European (non-Finnish)
6 / 1,180,006
0.00051%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain Significance by ClinGen Glaucoma Variant Curation Expert Panel (expert panel). (ClinVarID = 2442275)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.205. BayesDel score = -0.343469.
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots