Starting
Initialising…
0%
NRAS
Final classification
VUS
NRAS c.291-8G>A · p.?
NRAS

NM_002524.4:c.291-8G>A is an intronic variant in NRAS (intron 2, c.291-8).

Gene
NRAS
Transcript
NM_002524.4
HGVS · transcript:coding
NM_002524.4:c.291-8G>A
Consequence
N/A
GRCh38
chr1:114709736 C>T
GRCh37
chr1:115252357 C>T
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NRAS Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; no rule matched the adjudicated criteria.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NRAS Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: BP4 supporting benign, BP6 supporting benign, BP7 supporting benign; no rule matched the adjudicated criteria.
Classification rationale
BP4BP6BP7 VUS
NRAS c.291-8G>A

NM_002524.4:c.291-8G>A is an intronic variant in NRAS (intron 2, c.291-8). The ClinGen RASopathy Expert Panel VCEP v2.3.0 was applied as the primary classification framework.1 No pathogenic criteria were met. PVS1, PS1, PS5, PM1, PM5, PP2, PP4, PP5, BS3, BP1, BP3, BP6, PM3, and PM4 are not applicable to this intronic variant per VCEP specifications.2 Two benign supporting criteria are met: BP4 (SpliceAI predicts no splicing impact; max delta 0.01; predicted outcome does not match gain-of-function disease mechanism) and BP7 (intronic variant at non-canonical position with no predicted splice effect).3 The variant is present in gnomAD at low frequency: v2.1 AF=0.0064% (18/282,784 alleles), v4.1 AF=0.010% (167/1,607,416 alleles, 1 homozygote). These frequencies do not reach VCEP thresholds for BA1 (>=0.05%) or BS1 (>=0.025%), but the presence in population databases precludes PM2 (which requires absence from gnomAD).4 No de novo occurrences, functional studies, cosegregation data, or case-control enrichment have been reported for this variant in ClinVar or the published literature.5 Per VCEP Rule 19, >=2 supporting benign criteria (BP4 + BP7) classifies this variant as Likely Benign.6 This classification is concordant with the ClinGen RASopathy VCEP expert panel assessment of Likely Benign (ClinVar Variation ID 44575).7

BP4 + BP6 + BP7 VUS
2 cspec ↗pm5_candidates
6 cspec ↗final_classification_framework
Gene diagram · NM_002524.4 · variants mapped to exon structure
NRAS NM_002524.4
Fetching transcript structure from UCSC…
Applied criteria · 3 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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= 0.000103893; MAF= 0.01039%, 167/1607416 alleles, homozygotes = 1) and has highest observed frequency in the African/African American population (AF= 0.000147094; MAF= 0.01471%, 11/74782 alleles, homozygotes = 1); grpmax FAF= 9.991e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 6.36528e-05; MAF= 0.00637%, 18/282784 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000138466; MAF= 0.01385%, 1/7222 alleles, homozygotes = 0); grpmax FAF= 4.736e-05.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.01% · 167 / 1,607,416
      1 hom · FAF 0.01%
      African/African American
      11 / 74,782
      0.015%
      1 hom
      Remaining individuals
      8 / 62,280
      0.013%
      European (non-Finnish)
      136 / 1,174,060
      0.012%
      South Asian
      9 / 90,922
      0.0099%
      Ashkenazi Jewish
      1 / 29,572
      0.0034%
      East Asian
      1 / 44,858
      0.0022%
      Admixed American
      1 / 59,982
      0.0017%
      + 3 not observed (European (Finnish), Amish, Middle Eastern)
      gnomAD v2.1
      0.0064% · 18 / 282,784
      0 hom · FAF 0.0047%
      Remaining individuals
      1 / 7,222
      0.014%
      East Asian
      2 / 19,954
      0.01%
      European (non-Finnish)
      11 / 129,138
      0.0085%
      African/African American
      2 / 24,966
      0.008%
      South Asian
      2 / 30,600
      0.0065%
      + 3 not observed (Admixed American, Ashkenazi Jewish, European (Finnish))
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely benign (3 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Benign (1 clinical laboratory) and as Likely Benign by ClinGen RASopathy Variant Curation Expert Panel (expert panel). (ClinVarID = 44575)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      7Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Triaged references · 10 PMIDs not cited in assessment
      22220252 ↗ Prognostic Significance of NRAS Gene Mutations in Children with Acute Myelogenous Leukemia. CLINVAR
      24033266 ↗ A systematic approach to assessing the clinical significance of genetic variants. CLINVAR
      26980726 ↗ Comprehensive mutational profiling of core binding factor acute myeloid leukemia. CLINVAR
      27276561 ↗ Genomic Classification and Prognosis in Acute Myeloid Leukemia. CLINVAR
      29692343 ↗ Clonal interference of signaling mutations worsens prognosis in core-binding factor acute myeloid leukemia. CLINVAR
      17671181 ↗ Oncogenic NRAS, KRAS, and HRAS exhibit different leukemogenic potentials in mice. CLINVAR
      23325582 ↗ Massively parallel tumor multigene sequencing to evaluate response to panitumumab in a randomized phase III study of metastatic colorectal cancer. CLINVAR
      23708912 ↗ NRAS mutations with low allele burden have independent prognostic significance for patients with lower risk myelodysplastic syndromes. CLINVAR
      27069254 ↗ The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR