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HRAS
Final classification
VUS
HRAS c.403C>G · p.Arg135Gly
HRAS

NM_005343.4:c.403C>G (p.Arg135Gly) is a missense variant in HRAS, a RASopathy gene. Only one criterion is met: PP2 at supporting strength, which applies to all RASopathy missense variants per the ClinGen RASopathy VCEP specification.

Gene
HRAS
Transcript
NM_005343.4
HGVS · transcript:coding
NM_005343.4:c.403C>G
Consequence
N/A
GRCh38
chr11:533500 G>C
GRCh37
chr11:533500 G>C
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: PP2 supporting; combination = 1 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: PP2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PP2 VUS
HRAS c.403C>G

NM_005343.4:c.403C>G (p.Arg135Gly) is a missense variant in HRAS, a RASopathy gene. Only one criterion is met: PP2 at supporting strength, which applies to all RASopathy missense variants per the ClinGen RASopathy VCEP specification.1 This variant is present in gnomAD v4.1 at extremely low frequency (2/1,613,606 alleles, AF ~0.00012%), with single alleles observed in South Asian and European (non-Finnish) populations. It is absent from gnomAD v2.1 and gnomAD-Canada.2 This variant has been reported in ClinVar as Uncertain significance by a single clinical laboratory (GeneDx, VCID 3371962) with criteria provided. No expert panel review or pathogenic classification exists.3 Computational predictions are mixed: REVEL score 0.423 is intermediate, BayesDel score -0.136 leans benign, and SpliceAI predicts no splice impact (max delta 0.00). These do not converge on a consistent pathogenic or benign prediction.4 Position 135 is not within a VCEP-approved PM1 functional domain (P-loop residues 10-17; Switch I residues 25-40) and is not identified as a statistically significant hotspot by cancerhotspots.org.5 No functional studies have tested p.Arg135Gly in VCEP-approved assays (RAS Activation, MEK Activation, ERK Activation). The VCEP validation controls for HRAS are limited to G-domain residues (G12, G13, G60, K117, A146) and do not extend to position 135.6 No de novo occurrences, segregation data, or case-control studies exist for this variant. No literature publications were identified that mention this specific variant. With only PP2 (supporting) met and no other criteria fulfilled, this variant is classified as a Variant of Uncertain Significance (VUS) per the ACMG/AMP framework as modified by the ClinGen RASopathy VCEP.7

PP2 VUS
4 revelbayesdelspliceai ↗
5 vcep_alignment_with_pm1_domains_pptx
6 vcep_svi_rasopathy_vcep_v2_approved_functional_studies
Gene diagram · NM_005343.4 · variants mapped to exon structure
HRAS NM_005343.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 18 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PP2 supporting Pathogenic
PP2 is explicitly applicable to all RASopathy genes per the VCEP specification. HRAS is a RASopathy gene where missense variants are a common mechanism of disease, and this variant is a missense change (p.Arg135Gly).
VCEP states: 'PP2 is applicable to all RASopathy genes described and curated herein.' HRAS is a RASopathy genevariant is missense.
Assessed · not applied
Pathogenic
PS1 No evidence that p.Arg135Gly has been previously established as a pathogenic variant per VCEP criteria.
PS2 No de novo occurrence data is available for this variant.
PS3 VCEP-approved functional assays (RAS Activation, MEK Activation, ERK Activation) exist for HRAS, but the specific variant p.Arg135Gly has not been tested in any approved study.
PS4 No confirmed independent occurrences of this variant in individuals with RASopathy phenotypes.
PM1 Position 135 is not within a VCEP-approved functional domain.
PM2 VCEP PM2 requires complete absence from all population databases.
PM5 No candidate pathogenic missense variants at Arg135 were identified.
PM6 No de novo data (with or without parentage confirmation) is available for this variant.
PP1 No co-segregation data is available.
PP3 Computational evidence is mixed and does not consistently support a deleterious effect.
Benign
BA1 VCEP BA1 threshold is allele frequency ≥0.05%.
BS1 VCEP BS1 threshold is allele frequency ≥0.025%.
BS2 VCEP BS2 specifically states that general population data should not be used; it requires well-phenotyped family members.
BS3 No functional studies demonstrating no damaging effect exist for p.Arg135Gly.
BS4 No segregation data is available for this variant.
BP2 No data on trans or cis phase with a pathogenic variant is available.
BP4 Computational evidence is mixed and does not consistently suggest no impact on the gene product.
BP5 No evidence that this variant has been observed in a case with an alternate molecular basis for disease.
N/A · 9 PVS1 · PM3 · PM4 · 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= 1.23946e-06; MAF= 0.00012%, 2/1613606 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09784e-05; MAF= 0.00110%, 1/91088 alleles, homozygotes = 0).
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 / 1,613,606
0 hom
South Asian
1 / 91,088
0.0011%
European (non-Finnish)
1 / 1,179,976
8.5e-05%
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, 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 (1 clinical laboratory). (ClinVarID = 3371962)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.423. BayesDel score = -0.136316.
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. HRAS, a GTPase, is altered in a diverse range of cancers including head and neck squamous cell carcinoma, thyroid, and bladder cancer.
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