Variant classification summary

NM_002524.5:c.101C>T

NRAS · NP_002515.1:p.(Pro34Leu) · NM_002524.5

GRCh37: chr1:115258681 G>A · GRCh38: chr1:114716060 G>A

Gene: NRAS Transcript: NM_002524.5

Final call

VUS

PM1 moderate PM2 moderate PP2 supporting

Variant details

Gene

NRAS

Transcript

NM_002524.5

Protein

NP_002515.1:p.(Pro34Leu)

gnomAD AF

ClinVar

Pathogenic

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_002524.5:c.101C>T (p.Pro34Leu) in NRAS is a missense variant located in the Switch I functional domain, a VCEP-approved critical domain per the RASopathy Expert Panel supplemental material.

2

This variant is completely absent from gnomAD v2.1, v4.1, and gnomAD-Canada, satisfying the RASopathy VCEP PM2 requirement of complete absence from all population databases.

3

PP2 applies by VCEP rule, as missense variants in RASopathy genes have a low rate of benign missense variation.

4

PVS1, PP4, PP5, and BP6 are not applicable per explicit RASopathy VCEP specification.

5

No PS3 functional data from VCEP-approved assays are available for this specific variant; OncoKB reports Unknown Oncogenic Effect. The somatic observation in keratinocytic epidermal nevi (PMID:22499344) does not meet VCEP functional study requirements.

6

No germline RASopathy probands, de novo events, or segregation data have been identified for this variant in the literature reviewed; PS4, PS2, PM6, and PP1 are not met.

7

REVEL score of 0.845 supports a deleterious effect, but BayesDel (0.347) and SpliceAI (0.00) do not provide additional independent lines, so PP3 is not met.

8

Applying the generic ACMG/AMP 2015 classification framework (PMID:25741868) as a fallback due to the absence of RASopathy VCEP-specific final combination rules: two moderate criteria (PM1, PM2) and one supporting criterion (PP2) do not reach the threshold for Likely Pathogenic classification (requires e.g., 3 moderate, or 2 moderate + 2 supporting, or 1 strong + 1-2 moderate). This variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	LOF and/or haploinsufficiency has not been clearly identified as a disease mechanism for NRAS relative to the RASopathy spectrum phenotype; the RASopathy VCEP explicitly designates PVS1 as not applicable for this gene.	cspec
PS1	Not met	No previously established pathogenic variant resulting in the same amino acid change (p.Pro34Leu) at this residue in NRAS or in analogous Group 1 genes (HRAS, KRAS) has been identified. The somatic NRAS p.P34L observation in keratinocytic epidermal nevi (PMID:22499344) does not constitute a germline pathogenic variant established per RASopathy VCEP criteria.	cspec PMID:22499344
PS2	Not met	No de novo occurrence with confirmed paternity identified in the literature reviewed for this case.
PS3	Not met	The RASopathy VCEP limits PS3 to approved functional studies listed in the supplemental material. The approved assays for NRAS (RAS Activation, MEK Activation, ERK Activation, AKT Phosphorylation) reference PMIDs 19966803, 28594414, and 21263000, none of which are in this case's publication set. The somatic observation of NRAS p.P34L in keratinocytic epidermal nevi (PMID:22499344) confirms this variant can occur as an activating somatic mutation, but this is not a VCEP-approved functional study. OncoKB reports Unknown Oncogenic Effect for this variant.	cspec oncokb PMID:22499344
PS4	Not met	The only report of this variant is in a somatic mosaic context (keratinocytic epidermal nevus, PMID:22499344), which does not meet the VCEP definition of an independent occurrence in a germline RASopathy proband. No germline RASopathy cases with this variant have been documented.	PMID:22499344
PS5	N/A	The RASopathy VCEP does not define PS5. PS5 is a very-strong extension of PP5 (reputable source reports variant as pathogenic), and the VCEP explicitly designates PP5 as not for use per ClinGen SVI VCEP Review Committee recommendation.	cspec
PM1	Met	Residue Pro34 is located within the Switch I domain of NRAS (analogous to HRAS aa 25-40), which is a VCEP-approved critical functional domain per the supplemental material (Alignment-with-PM1-domains.pptx). Switch I is essential for GTP binding and effector interactions in RAS proteins. The VCEP explicitly permits PM1 application across analogous residues in Group 1 genes (HRAS, NRAS, KRAS). The variant substitutes proline with leucine, altering a residue within this well-established functional domain.	cspec vcep_alignment_with_pm1_domains_pptx
PM2	Met	NM_002524.5:c.101C>T is completely absent from all population databases queried (gnomAD v2.1, gnomAD v4.1, gnomAD-Canada v1.0), satisfying the RASopathy VCEP requirement that the variant must be completely absent from all population databases.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	NM_002524.5:c.101C>T (p.Pro34Leu) is a missense variant eligible for PM5 consideration under the VCEP rule, which requires a previously established pathogenic missense variant at the same residue (or analogous residue in Group 1 genes HRAS, NRAS, KRAS). No pathogenic missense variant at NRAS P34 has been identified in ClinVar, literature, or the analogous residues in HRAS/KRAS. The somatic NRAS p.P34L observation in KEN (PMID:22499344) does not establish the residue as harboring a germline pathogenic variant.	cspec clinvar PMID:22499344
PM6	Not met	No de novo report for this variant, with or without confirmation of paternity/maternity, was identified in the literature reviewed.
PP1	Not met	No segregation data are available for this variant. The RASopathy VCEP requires at least three informative meioses to apply PP1 at any strength.
PP2	Met	The RASopathy VCEP explicitly states that PP2 is applicable to all RASopathy genes described and curated in its scope, including NRAS. This is a missense variant in a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease.	cspec
PP3	Not met	The RASopathy VCEP requires multiple lines of computational evidence supporting a deleterious effect. REVEL score of 0.845 provides one line supporting pathogenicity, but BayesDel at 0.347 does not reach a clear threshold, and SpliceAI delta is 0.00 (no splice impact). Only one computational tool (REVEL) unambiguously supports a deleterious effect, which does not satisfy the VCEP requirement for multiple independent computational lines.	revel bayesdel spliceai
PP4	N/A	The RASopathy VCEP explicitly designates PP4 as not applicable for RASopathies, directing use of PS4 for proband counting instead.	cspec
PP5	N/A	The RASopathy VCEP explicitly designates PP5 as not for use, per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.	cspec
BA1	Not met	The variant is absent from all population databases queried, with an allele frequency of 0, well below the RASopathy VCEP BA1 threshold of ≥0.05% (5e-4).	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from all population databases queried, well below the RASopathy VCEP BS1 threshold of ≥0.025%.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	The RASopathy VCEP instructs that general population data should not be used for BS2 due to variable expressivity and severity. Clinical laboratories are encouraged to accumulate more than 3 instances of well-phenotyped family members before applying this criterion. No such data are available for this variant.	cspec
BS3	Not met	No VCEP-approved functional study demonstrates a benign effect for this variant. The approved assays and their associated PMIDs are not available in the case publication set.	cspec
BS4	Not met	No segregation data available to assess lack of segregation in affected family members. The RASopathy VCEP requires one informative meiosis.
BP1	N/A	The RASopathy VCEP specifies BP1 applies to truncating variants (nonsense, frameshift, canonical splice sites, initiation codon, gene deletions) in genes without established LOF correlation. NRAS p.Pro34Leu is a missense variant, and the RASopathy disease mechanism is gain-of-function, not loss-of-function.	cspec
BP2	Not met	No evidence that this variant has been observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in any inheritance pattern.
BP4	Not met	The RASopathy VCEP requires multiple lines of computational evidence suggesting no impact. REVEL score of 0.845 indicates a deleterious effect, contradicting the requirements for BP4. BayesDel at 0.347 is borderline, and SpliceAI delta is 0.00. The computational evidence does not support a conclusion of no impact.	revel bayesdel spliceai
BP5	Not met	No evidence that this variant has been found in a case with an alternate molecular basis for disease.
BP6	N/A	The RASopathy VCEP explicitly designates BP6 as not for use, per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.	cspec
BP7	N/A	BP7 applies to synonymous (silent) variants. NM_002524.5:c.101C>T is a missense variant (p.Pro34Leu), not synonymous.
BP3	N/A	Substitution variant; BP3 applies to in-frame deletions/insertions in repetitive regions.
PM3	N/A	Substitution variant, and RASopathy VCEP designates PM3 as not applicable for RASopathies.	cspec
PM4	N/A	Substitution variant; PM4 applies to in-frame deletions/insertions and stop-loss variants.

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