Variant classification summary

NM_002524.4:c.35G>A

NRAS · NP_002515.1:p.(Gly12Asp) · NM_002524.4

GRCh37: chr1:115258747 C>T · GRCh38: chr1:114716126 C>T

Gene: NRAS Transcript: NM_002524.4

Final call

Likely Pathogenic

PS1 strong PS4 supporting PM1 moderate PP3 supporting

Variant details

Gene

NRAS

Transcript

NM_002524.4

Protein

NP_002515.1:p.(Gly12Asp)

gnomAD AF

1.0533124818768293e-05 (v4.1)

ClinVar

Pathogenic

OncoKB

Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_002524.4:c.35G>A (p.Gly12Asp) is the same amino acid change as well-established pathogenic G12D variants in HRAS, KRAS, and other RAS genes, meeting PS1 at Strong strength per RASopathy VCEP rules.

2

Gly12 is located in the P-loop domain (amino acids 10-17), a VCEP-specified critical functional domain and mutational hotspot without benign variation, meeting PM1 at Moderate strength.

3

REVEL score of 0.783 meets the VCEP PP3 threshold of ≥0.7 for missense variants, providing Supporting in silico evidence of pathogenicity.

4

NRAS G12D has been observed in multiple probands with RASopathy-spectrum phenotypes including juvenile myelomonocytic leukemia, meeting PS4 at Supporting strength (≥1 point).

5

The variant is present at extremely low frequency in gnomAD (max AF=0.0046%), far below BA1 (0.05%) and BS1 (0.025%) thresholds, but does not meet PM2 which requires complete absence from gnomAD per VCEP rules.

6

Extensive functional evidence for NRAS G12D exists in the literature including mouse models and biochemical assays, but VCEP-approved functional assay verification for the specific variant in germline RASopathy context requires human review.

Final determination: Rule11 in the ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NRAS Version 2.3.0 v2.3.0 criteria-combination framework is satisfied by the adjudicated criteria, so the variant is classified as Likely Pathogenic.

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	PVS1 is classified as Not Applicable by the ClinGen RASopathy VCEP for NRAS (v2.3.0). NM_002524.4:c.35G>A is a missense variant (p.Gly12Asp), not a null variant, and does not fall into any PVS1 variant bucket.	cspec
PS1	Met	NM_002524.4:c.35G>A (p.Gly12Asp) is the same amino acid change as well-established pathogenic G12D variants in HRAS, KRAS, and other RAS genes, satisfying the RASopathy VCEP PS1 rule for analogous pathogenic residue positions. ClinVar classifies NRAS G12D as Pathogenic (11 clinical laboratories) and Likely pathogenic (3 laboratories).	cspec clinvar
PS2	Not met	No de novo occurrence data (with confirmed maternity and paternity) is available for NM_002524.4:c.35G>A in this evidence packet. VCEP PS2 requires point-based scoring from documented de novo events.	cspec
PS3	Not assessed	Extensive functional evidence for NRAS G12D as a gain-of-function variant exists in the literature (multiple mouse models, RAS activation assays, MEK/ERK phosphorylation assays, focus formation assays). OncoKB curates this variant as Oncogenic/Gain-of-function. However, specific VCEP-approved functional assay instances (RAS Activation Assay PMIDs: 19966803, 28594414, 21263000; MEK Activation Assay: same PMIDs) could not be verified for this exact variant. The approved full-text papers (PMID:19075190, 25252692, 21586752, 23687087, 18372904) demonstrate N-Ras G12D functional impact but are primarily somatic/cancer contexts, not germline RASopathy contexts. Needs human review to determine if these meet the VCEP PS3 threshold.	cspec oncokb PMID:19075190 PMID:25252692 PMID:21586752 PMID:23687087 PMID:18372904
PS4	Met	NRAS G12D has been observed in multiple probands with RASopathy-spectrum phenotypes. ClinVar reports 14 usable submissions including clinical laboratories classifying as Pathogenic. G12D is reported in juvenile myelomonocytic leukemia (JMML), a RASopathy-associated condition (PMID:17332249). Meeting VCEP PS4 threshold of at least 1 point (Supporting).	cspec clinvar PMID:16434492
PM1	Met	Gly12 is located in the P-loop domain (amino acids 10-17), one of four critical and well-established functional domains specified by the RASopathy VCEP (P-loop, SW1, SW2, SAK). The P-loop is a mutational hotspot without benign variation, satisfying PM1 at Moderate strength.	cspec
PM2	Not met	The RASopathy VCEP PM2 rule requires the variant to be absent from gnomAD controls. NM_002524.4:c.35G>A is present in gnomAD v2.1 (AF=7.95e-6; 2/251,484 alleles) and gnomAD v4.1 (AF=1.05e-5; 17/1,613,956 alleles). It does not meet the VCEP requirement for absence from controls.	cspec gnomad_v2 gnomad_v4
PM5	Not met	PM5 is designed for novel missense changes at a codon where a different pathogenic missense is already established. NM_002524.4:c.35G>A (p.Gly12Asp) is itself one of the most well-characterized pathogenic changes at codon 12, not a novel variant. Applying PM5 to the index pathogenic variant would constitute double-counting with PS1. Multiple other pathogenic changes at codon 12 (G12V, G12C, G12S, G12A, G12R) are well-established, but PM5 is not applied to the reference pathogenic change.	cspec
PM6	Not met	No de novo data (without confirmation of maternity and paternity) is available for this variant. VCEP PM6 requires point-based scoring from de novo observations. No de novo events are reported in ClinVar, literature, or case materials.	cspec
PP1	Not met	No segregation data is available for NM_002524.4:c.35G>A. VCEP PP1 requires at least 3 informative meioses for Supporting strength. No family studies or cosegregation data are present in the evidence packet.	cspec
PP2	N/A	PP2 is classified as Not Applicable by the ClinGen RASopathy VCEP for NRAS (v2.3.0).	cspec
PP3	Met	REVEL score is 0.783, which meets the RASopathy VCEP PP3 threshold of ≥0.7 for missense variants. SpliceAI predicts no splice impact (max delta=0.00), consistent with a missense mechanism rather than splicing effect. BayesDel score (0.329) is below typical pathogenic thresholds but REVEL is the specified VCEP metric.	cspec revel spliceai
PP4	N/A	PP4 is classified as Not Applicable by the ClinGen RASopathy VCEP for NRAS (v2.3.0).	cspec
PP5	N/A	PP5 is classified as Not Applicable by the ClinGen RASopathy VCEP for NRAS (v2.3.0).	cspec
BA1	Not met	The maximum gnomAD filtering allele frequency for NM_002524.4:c.35G>A is 4.62e-5 (0.0046%) in the European (Finnish) subpopulation (v2.1) and grpmax FAF is 7.63e-6 (v4.1). These are far below the VCEP BA1 threshold of ≥0.05% (Stand Alone). The variant is too rare in population databases to meet BA1.	cspec gnomad_v2 gnomad_v4
BS1	Not met	The maximum gnomAD allele frequency for NM_002524.4:c.35G>A (0.0046%) is below the VCEP BS1 threshold of ≥0.025%. The variant is not sufficiently common in population databases to meet BS1 at Strong strength.	cspec gnomad_v2 gnomad_v4
BS2	Not met	No data on healthy adult individuals carrying NM_002524.4:c.35G>A is available. VCEP BS2 uses point-based scoring requiring documented healthy homozygote or heterozygote individuals. No such observations are present in the evidence packet.	cspec
BS3	N/A	BS3 is classified as Not Applicable by the ClinGen RASopathy VCEP for NRAS (v2.3.0).	cspec
BS4	Not met	No segregation data is available. VCEP BS4 requires at least one informative meiosis demonstrating lack of cosegregation with disease. No family studies are present in the evidence packet.	cspec
BP1	N/A	BP1 applies only to truncating variants (nonsense, frameshift, canonical splice site, initiation codon, or gene deletions) in genes where the disease mechanism is gain-of-function. NM_002524.4:c.35G>A is a missense variant (p.Gly12Asp), not a truncating variant. BP1 does not apply to missense changes.	cspec
BP2	Not met	No evidence of an alternative molecular cause for a RASopathy in the same gene is available. VCEP BP2 requires point-based scoring for an alternative molecular cause. No such data is present in the evidence packet.	cspec
BP4	Not met	REVEL score is 0.783, which does not meet the VCEP BP4 threshold of ≤0.3 for missense variants. Multiple in silico predictors support a deleterious effect rather than a benign impact.	cspec revel bayesdel
BP5	Not met	No evidence of an alternative molecular cause for disease is available. VCEP BP5 uses point-based scoring requiring an alternative molecular cause. No such observations are present in the evidence packet.	cspec
BP6	N/A	BP6 is classified as Not Applicable by the ClinGen RASopathy VCEP for NRAS (v2.3.0).	cspec
BP7	N/A	BP7 applies only to synonymous (silent) variants with no predicted splice impact and low nucleotide conservation. NM_002524.4:c.35G>A is a missense variant (p.Gly12Asp), not a synonymous variant. BP7 does not apply to missense changes.	cspec

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