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NRAS
Final classification
VUS
NRAS c.38G>T · p.Gly13Val
NRAS

c.38G>T (p.Gly13Val) is located in the P-loop domain (residues 10-17), an approved functional domain critical for GTP binding and hydrolysis in NRAS, satisfying PM1 at moderate strength per the ClinGen RASopathy VCEP.

Gene
NRAS
Transcript
NM_002524.5
HGVS · transcript:coding
NM_002524.5:c.38G>T
Consequence
N/A
GRCh38
chr1:114716123 C>A
GRCh37
chr1:115258744 C>A
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.0 v1.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PP2 supporting, PP3 supporting; combination = 1 moderate + 2 supporting, which maps to VUS.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.0 v1.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PP2 supporting, PP3 supporting; combination = 1 moderate + 2 supporting, which maps to VUS.
Classification rationale
PM1PP2PP3 VUS
NRAS c.38G>T

c.38G>T (p.Gly13Val) is located in the P-loop domain (residues 10-17), an approved functional domain critical for GTP binding and hydrolysis in NRAS, satisfying PM1 at moderate strength per the ClinGen RASopathy VCEP.1 PP2 is met at supporting strength as this is a missense variant in NRAS, a RASopathy gene where missense variants are a common mechanism of disease, per the VCEP specification.2 Multiple in silico tools predict a deleterious effect (REVEL = 0.789, BayesDel = 0.314), satisfying PP3 at supporting strength per the VCEP.3 The variant is present at extremely low frequency in gnomAD (v2.1: 1/251,492; v4.1: 1/1,614,026) and is absent from gnomAD-Canada, consistent with a rare disease-causing variant, though PM2 is not met per strict VCEP requirement for complete absence.4 The variant has been reported in ClinVar as Likely pathogenic by two clinical laboratories (ClinVar ID 375876) and is annotated as Likely Oncogenic by OncoKB with 141 somatic occurrences in COSMIC, supporting its functional significance, though these alone do not independently meet PS4 or PS5 criteria per VCEP rules.5 PVS1, PP5, BP6, PP4 are not applicable per the RASopathy VCEP specification. BP1 is not applicable as this is a missense variant, not a truncating variant. BP7 is not applicable as this is not a synonymous variant.6

PM1 + PP2 + PP3 VUS
1 cspec ↗vcep_alignment_with_pm1_domains_pptxoncokb ↗
3 revelbayesdel
Gene diagram · NM_002524.5 · variants mapped to exon structure
NRAS NM_002524.5
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 16 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
Gly13 in NRAS lies within the P-loop domain (residues 10-17 in HRAS, analogous in NRAS), which is an approved functional domain in the RASopathy VCEP supplemental material (Alignment with PM1 domains). This is also a statistically significant mutational hotspot per cancerhotspots.org. The VCEP specifies moderate strength for PM1 application at approved functional domains. The P-loop is critical for nucleotide binding and GTPase activity.
P-loop domain (residues analogous to HRAS 10-17) is VCEP-approved PM1 domainGly13 lies within the P-loopStatistically significant hotspot per cancerhotspots.org
PP2 supporting Pathogenic
The RASopathy VCEP states that PP2 is applicable to all RASopathy genes described and curated. NRAS is a RASopathy gene with a low rate of benign missense variation where missense variants are a common mechanism of disease. This is a missense variant (p.Gly13Val).
VCEP: PP2 is applicable to all RASopathy genesNRAS is a RASopathy geneVariant is missense
PP3 supporting Pathogenic
Multiple lines of computational evidence support a deleterious effect. REVEL score of 0.789 predicts damaging. BayesDel score of 0.314 supports a deleterious effect. SpliceAI delta score of 0.00 indicates no splicing impact. The VCEP specifies supporting strength for PP3 when multiple lines of computational evidence support a deleterious effect.
REVEL score: 0.789 (damaging)BayesDel score: 0.314 (supports deleterious)SpliceAI max delta: 0.00 (no splice impact)
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change (p.Gly13Val) to have been previously established as pathogenic per VCEP criteria via a different nucleotide change.
PS2 PS2 requires a confirmed de novo occurrence (paternity confirmed) in a patient with RASopathy and no family history.
PS3 The RASopathy VCEP requires approved functional studies supporting a damaging effect at Strong strength.
PS4 PS4 requires counting independent proband occurrences.
PM2 The RASopathy VCEP requires complete absence from all population databases.
PM5 The RASopathy VCEP PM5 rule states it should not be used as an independent criterion in conjunction with PM1 when the residue is a designated mutational hot-spot.
PM6 PM6 requires a confirmed de novo observation without confirmation of paternity and maternity.
PP1 PP1 requires co-segregation data with at least three informative meioses per VCEP (supporting level).
Benign
BA1 The RASopathy VCEP sets the BA1 threshold at allele frequency ≥0.05%.
BS1 The RASopathy VCEP sets the BS1 threshold at allele frequency ≥0.025%.
BS2 The RASopathy VCEP states that general population data should not be used for BS2 due to variable expressivity and severity of RASopathies.
BS3 BS3 requires approved functional studies showing no damaging effect on protein function.
BS4 The RASopathy VCEP requires only one informative meiosis to apply BS4 at strong strength.
BP2 BP2 requires observation in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant.
BP4 BP4 requires multiple lines of computational evidence suggesting no impact on gene or gene product.
BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease.
N/A · 7 PVS1 · PP4 · PP5 · BP1 · BP3 · 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= 6.19569e-07; MAF= 0.00006%, 1/1614026 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47535e-07; MAF= 0.00008%, 1/1179892 alleles, homozygotes = 0).
v2.1
This variant is present in gnomAD v2.1 (AF= 3.97627e-06; MAF= 0.00040%, 1/251492 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.78997e-06; MAF= 0.00088%, 1/113766 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
6.2e-05% · 1 / 1,614,026
0 hom
European (non-Finnish)
1 / 1,179,892
8.5e-05%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0004% · 1 / 251,492
0 hom
European (non-Finnish)
1 / 113,766
0.00088%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Likely pathogenic (2 clinical laboratories). (ClinVarID = 375876)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.789. BayesDel score = 0.314125.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV54736480, n = 141 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
2papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & References.
The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants.
Searched
c.38G>TG13VGly13ValG13Gly13NRAS
Found
Crystal structure of the Ras-RasGAP complex at 2.5 Å resolution. Glycine-12 is identified as within van der Waals distance of both Arg789 of GAP-334 and Gln61 of Ras; even its mutation to alanine would disrupt transition-state arrangements. Glycine-13 is noted as more remote from GAP-334. The P-loop (residues 10-16) is characterized as critical for phosphate binding and GTPase activity.
Variant
◇ Residue / gene-level — variant not named
Applied to
PM1 supports · met
Why
Provides structural rationale for the functional importance of the P-loop domain containing Gly13. Referenced in PM1 assessment as domain-level evidence, but does not mention the G13V variant specifically.
Glycine-13 is more remote from GAP-334.
Location Results; Figure 4C and caption  ·  Context X-ray crystallography of H-Ras-GDP-AlF3-GAP-334 complex  ·  full text
PMID PMID:9219684
Found
Structured finding pending for this record — see source link.
Applied to
PM1 supports · met
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
20371679 ↗ RAS mutations contribute to evolution of chronic myelomonocytic leukemia to the proliferative variant. ONCOKB
26619011 ↗ Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. ONCOKB
28572459 ↗ AACR Project GENIE: Powering Precision Medicine through an International Consortium. ONCOKB
33637626 ↗ Differential Outcomes in Codon 12/13 and Codon 61 NRAS-Mutated Cancers in the Phase II NCI-MATCH Trial of Binimetinib in Patients with NRAS-Mutated Tumors. ONCOKB
16434186 ↗ Mutational analysis of PDGFR-RAS/MAPK pathway activation in childhood medulloblastoma. CLINVAR
24436047 ↗ Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR