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
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).
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
BP4 + BP6 + BP7
→
VUS
Gene diagram
· NM_002524.4 · variants mapped to exon structure
NRAS
NM_002524.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 13 assessed
Applied · 3
Strength
Supporting
Moderate
Strong
Very strong
✓
BP4
supporting
Benign
SpliceAI predicts no splicing impact (max delta score = 0.01). The predicted splicing outcome is negligible and does not support a gain-of-function disease mechanism for RASopathies. Per VCEP BP4 instructions, this criterion is applicable for splicing variants where the predicted outcome is negligible or does not match the disease mechanism.
SpliceAI max delta = 0.01predicting no splice-altering effectREVEL not applicable for intronic variant
✓
✓
BP7
supporting
Benign
c.291-8G>A is an intronic variant at position -8 from exon 3 (not a canonical splice site). SpliceAI predicts no impact to the splice consensus sequence nor the creation of a new splice site (max delta = 0.01). Per VCEP BP7, this rule is applicable for intronic positions except canonical splice sites and should be used in conjunction with BP4.
SpliceAI max delta = 0.01no predicted donor/acceptor gain or lossvariant is at intronic position -8
Assessed · not applied
Pathogenic
PS2
No de novo occurrence with confirmed maternity and paternity has been reported for NM_002524.4:c.291-8G>A in ClinVar submissions or the published literature.
PS3
No functional studies from the VCEP-approved assay list (RAS activation, MEK/ERK activation assays) have been performed on c.291-8G>A.
PS4
The variant is present in gnomAD at 167/1,607,416 alleles (v4.1, AF=0.010%), including one homozygote.
PM2
VCEP PM2 requires the variant be absent from gnomAD.
PM6
No assumed de novo observation (without confirmed parentage) has been reported for this variant in ClinVar or the literature.
PP1
No cosegregation data with disease in multiple affected family members has been reported for c.291-8G>A.
PP3
SpliceAI predicts no splicing impact (max delta score = 0.01), which does not support a deleterious effect.
Benign
BA1
VCEP BA1 requires gnomAD filtering allele frequency >= 0.05%.
BS1
VCEP BS1 requires gnomAD filtering allele frequency >= 0.025%.
BS2
No observation of this variant in a healthy adult individual (homozygous or heterozygous) with documented unaffected clinical status has been reported.
BS4
No published data demonstrate lack of segregation of c.291-8G>A in affected members of a family.
BP2
No evidence of c.291-8G>A observed in trans with a known pathogenic NRAS variant, or as an alternative molecular cause for a RASopathy phenotype.
BP5
No alternative molecular cause for a RASopathy has been identified in cases carrying c.291-8G>A.
N/A · 9
PVS1 · PS1 · PM1 · PM5 · PP2 · PP4 · PP5 · BS3 · BP1
Research & evidence
Population frequency
gnomAD v4.1
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%
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%
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
0 hom
Not observed in any ancestry group.
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)
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.
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.
Sources & reference links
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
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