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Classification rationale
1

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

2

The ClinGen RASopathy Expert Panel VCEP v2.3.0 was applied as the primary classification framework.

cspec ↗
3

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.

cspec ↗
4

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).

spliceai ↗ cspec ↗
5

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).

gnomad_v2 ↗ gnomad_v4 ↗
6

No de novo occurrences, functional studies, cosegregation data, or case-control enrichment have been reported for this variant in ClinVar or the published literature.

clinvar ↗
7

Per VCEP Rule 19, >=2 supporting benign criteria (BP4 + BP7) classifies this variant as Likely Benign.

cspec ↗
8

This classification is concordant with the ClinGen RASopathy VCEP expert panel assessment of Likely Benign (ClinVar Variation ID 44575).

clinvar ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
Rationale
Select a criterion to inspect its explanation.
Evidence used
Gaps remaining
Rule
Publications
Research and evidence
gnomAD v2.1 evidence
v2.1
gnomAD v4.1 evidence
v4.1
01
Population
gnomAD v2.1This 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.
gnomAD v4.1This 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.
gnomAD CanadaAvailable
ClinVar evidence
02
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)
03
Functional
No functional summary recorded.
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
COSMIC evidence
05
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
06
Cancer hotspots
No cancer hotspot summary recorded.