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GNAQ
Final classification
VUS
GNAQ c.289C>T · p.Leu97Phe
GNAQ

NM_002072.5:c.289C>T (p.Leu97Phe) is a missense variant in GNAQ, a G protein alpha subunit gene recurrently mutated in uveal melanoma.

Gene
GNAQ
Transcript
NM_002072.5
HGVS · transcript:coding
NM_002072.5:c.289C>T
Consequence
N/A
GRCh38
chr9:77922193 G>A
GRCh37
chr9:80537109 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate, PP3 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 moderate, PP3 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
GNAQ c.289C>T

NM_002072.5:c.289C>T (p.Leu97Phe) is a missense variant in GNAQ, a G protein alpha subunit gene recurrently mutated in uveal melanoma. This variant is extremely rare in population databases, observed in only 2 of 1,613,556 alleles in gnomAD v4.1 (allele frequency 1.24e-06), and is absent from gnomAD v2.1 and gnomAD-Canada v1.0.1 In silico prediction tools provide supporting evidence for a deleterious effect; REVEL scores the variant at 0.748, above the damaging threshold. BayesDel score is 0.306, which is below commonly used thresholds. SpliceAI predicts no splicing impact.2 The variant is absent from ClinVar and has not been reported in the literature as a germline variant. It has been observed in 2 somatic cancer samples in COSMIC (COSV105143328).3 No functional studies, de novo reports, cosegregation data, or case-control data are available for this variant. Residue Leu97 is not within a known GNAQ mutational hotspot (canonical driver residues are Gln209 and Arg183).4 The only applicable criteria are PM2 (moderate, based on extreme rarity in population databases) and PP3 (supporting, based on in silico prediction). No other pathogenic or benign criteria are met. With only one moderate criterion (PM2) and one supporting criterion (PP3) met, the overall evidence is insufficient to classify this variant as pathogenic or likely pathogenic under ACMG/AMP 2015 rules. The classification is Variant of Uncertain Significance (VUS).5

PM2 + PP3 VUS
2 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_002072.5 · variants mapped to exon structure
GNAQ NM_002072.5
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 22 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
NM_002072.5:c.289C>T is extremely rare in population databases. In gnomAD v4.1, the variant is observed at an allele frequency of 1.24e-06 (2/1,613,556 alleles, 0 homozygotes; grpmax FAF=4.43e-06), far below the 0.1% PM2 threshold. The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0.
gnomAD v4.1: 2/1613556 alleles (AF=1.24e-06
PP3 supporting Pathogenic
In silico prediction tools support a deleterious effect. REVEL score is 0.748 (above the 0.5 threshold for damaging prediction). BayesDel score is 0.306, which is below commonly used damaging thresholds. SpliceAI predicts no splicing impact (max delta = 0.00). The REVEL score provides supporting-level evidence for pathogenicity.
REVEL=0.748 (damaging). BayesDel=0.306 (borderline/low). SpliceAI max delta=0.00 (no splice impact).
Assessed · not applied
Pathogenic
PS1 No pathogenic variant with the same amino acid change (p.Leu97Phe) has been identified in ClinVar or the literature.
PS2 No de novo occurrence data is available for NM_002072.5:c.289C>T.
PS3 No variant-specific functional data exists for NM_002072.5:c.289C>T (p.Leu97Phe).
PS4 No case-control or prevalence data comparing affected versus unaffected individuals is available for this variant in GNAQ-associated disease.
PM1 Residue Leu97 is not located within a well-characterized critical functional domain with established pathogenic missense constraint.
PM5 No pathogenic missense variant at the same residue (Leu97) with a different amino acid change was identified in ClinVar.
PM6 No de novo reports exist for NM_002072.5:c.289C>T.
PP1 No cosegregation data is available.
PP2 While GNAQ has known pathogenic missense variants (e.g., p.Gln209Leu/Pro, p.Arg183Gln/Cys), no gene-level missense constraint metrics (e.g., gnomAD missense Z-score, o/e ratio) are available in the evidence to determine whether GNAQ has a low rate of benign missense variation sufficient to meet PP2.
PP4 No patient phenotype data is available to assess whether the variant carrier's phenotype is highly specific for GNAQ-associated disease.
PP5 NM_002072.5:c.289C>T is absent from ClinVar.
Benign
BA1 The variant allele frequency in gnomAD v4.1 is 1.24e-06 (0.000124%), far below the 1% BA1 threshold.
BS1 The variant allele frequency in gnomAD v4.1 is 1.24e-06 (0.000124%), far below the 0.3% BS1 threshold.
BS2 No data on healthy adult carriers is available to assess whether this variant has been observed in a homozygous or hemizygous state without disease.
BS3 No well-established functional studies demonstrate a benign effect for NM_002072.5:c.289C>T (p.Leu97Phe).
BS4 No segregation data is available to demonstrate lack of cosegregation with disease in affected family members.
BP1 GNAQ is known to harbor pathogenic missense variants (e.g., p.Gln209Leu, p.Arg183Gln) associated with uveal melanoma and other conditions.
BP2 No data on observation in trans with a pathogenic variant is available for this variant.
BP4 REVEL score of 0.748 is in the damaging range (>0.5), which does not support a benign in silico prediction.
BP5 No data is available indicating that this variant was observed in a case with an alternate molecular basis for disease.
BP6 NM_002072.5:c.289C>T is absent from ClinVar.
BP7 NM_002072.5:c.289C>T is a missense variant (p.Leu97Phe), not a synonymous variant with no predicted splice impact.
N/A · 4 PVS1 · PM3 · PM4 · BP3
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= 1.2395e-06; MAF= 0.00012%, 2/1613556 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 2.66823e-05; MAF= 0.00267%, 2/74956 alleles, homozygotes = 0); grpmax FAF= 4.43e-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
0.00012% · 2 / 1,613,556
0 hom · FAF 0.00044%
African/African American
2 / 74,956
0.0027%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, European (non-Finnish))
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.748. BayesDel score = 0.306198.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. GNAQ, a G protein subunit, is recurrently mutated in uveal melanoma.
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 previously been reported in somatic cancers (COSMIC; COSV105143328, n = 2 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots