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MYCL
Final classification
VUS
MYCL c.961C>G · p.Arg321Gly
MYCL

PM2 (Moderate): variant is at extremely low population frequency — gnomAD v2.1 AF 3.98e-06 and v4.1 AF 2.48e-06, well below the <0.1% threshold, zero homozygotes.

Gene
MYCL
Transcript
NM_001033082.2
HGVS · transcript:coding
NM_001033082.2:c.961C>G
Consequence
N/A
GRCh38
chr1:39897596 G>C
GRCh37
chr1:40363268 G>C
Basis VUS: only PM2 (moderate) and PP3 (supporting) are met, and that combination satisfies no pathogenic or benign rule under the generic ACMG/AMP 2015 framework.
VUS: only PM2 (moderate) and PP3 (supporting) are met, and that combination satisfies no pathogenic or benign rule under the generic ACMG/AMP 2015 framework.
Classification rationale
PM2PP3 VUS
MYCL c.961C>G

PM2 (Moderate): variant is at extremely low population frequency — gnomAD v2.1 AF 3.98e-06 and v4.1 AF 2.48e-06, well below the <0.1% threshold, zero homozygotes. PP3 (Supporting): REVEL 0.914 and BayesDel 0.499 both predict a deleterious missense effect. One moderate plus one supporting criterion meets no generic ACMG/AMP 2015 combination rule, yielding Variant of Uncertain Significance (VUS).

PM2 + PP3 VUS
Gene diagram · NM_001033082.2 · variants mapped to exon structure
MYCL NM_001033082.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
Met (moderate): gnomAD v2.1 AF 3.98e-06 and v4.1 AF 2.48e-06, both far below the <0.1% threshold, with zero homozygotes.
gnomAD v2.1: total AF 3.976e-06 (0.00040%, 1/251,494 alleles), 0 homozygotes, max subpop NFE AF 8.79e-06 (0.00088%)gnomAD v4.1: total AF 2.478e-06 (0.00025%, 4/1,614,198 alleles), 0 homozygotes, grpmax FAF 7.9e-07, max subpop NFE AF 3.39e-06 (0.00034%)gnomAD-Canada v1.0: variant absent
PP3 supporting Pathogenic
Met (supporting): REVEL 0.914 and BayesDel 0.499 both predict a deleterious missense effect.
REVEL v1.3 score 0.914 for NM_001033082.2:c.961C>G (deleterious prediction)BayesDel (noAF) score 0.499098 for chr1:40363268 G>C (deleterious prediction)SpliceAI max delta 0.01 (no splice impact; neutral for PP3 on this missense variant)
Assessed · not applied
Pathogenic
PS1 Not met: no alternate-nucleotide variant producing p.Arg321Gly is established as pathogenic; the only ClinVar record is this variant itself (VUS).
PS2 Not assessed: no proband, parental-testing, or trio data were available to evaluate a de novo occurrence.
PS3 Not assessed: no wet-lab functional study of this variant was available in either direction.
PS4 Not assessed: no case-control or cohort study of this variant exists to demonstrate enrichment in affected individuals.
PM1 Not met: no mutational hotspot or critical functional domain is documented at MYCL Arg321, and no benign-variation constraint was established.
PM3 Not assessed: no allele-phase or segregation data exist, and MYCL has no established autosomal-recessive germline disease association.
PM5 Not assessed: no alternate missense change at Arg321 is established as pathogenic; flagged for human review.
PM6 Not assessed: no proband observation or parental-testing status is available to evaluate an assumed de novo occurrence.
PP1 Not assessed: no pedigree, affected relatives, or segregation data exist for this variant.
PP2 Not met: missense is not MYCL's disease mechanism — it is activated by amplification — and no missense constraint data support a low benign-missense rate.
PP4 Not assessed: no proband phenotype or family history data were available.
PP5 Not met: no ClinVar expert-panel pathogenic classification exists for this exact variant — only a single-submitter laboratory VUS.
Benign
BA1 Not met: gnomAD v2.1 AF 3.98e-06 and v4.1 AF 2.48e-06 are orders of magnitude below the >1% BA1 threshold.
BS1 Not met: observed allele frequencies (max 0.00088%) are far below the >0.3% threshold, and no disease-allele expectation applies.
BS3 Not assessed: no functional study demonstrating normal function was available.
BS4 Not assessed: no family data exist to evaluate non-segregation in affected relatives.
BP1 Not met: MYCL is an oncogene activated by amplification, not a gene whose disease mechanism is truncation.
BP2 Not assessed: no pathogenic second variant or allele-phase data exist to evaluate cis/trans configuration.
BP4 Not met: REVEL 0.914 and BayesDel 0.499 both predict a deleterious effect, directly contradicting a no-impact conclusion.
BP5 Not assessed: no proband-level data on an alternate molecular basis for disease were available.
BP6 Not met: no ClinVar expert-panel benign or likely-benign classification exists for this exact variant.
N/A · 5 PVS1 · PM4 · BS2 · BP3 · BP7
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= 2.47801e-06; MAF= 0.00025%, 4/1614198 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.38971e-06; MAF= 0.00034%, 4/1180042 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.97624e-06; MAF= 0.00040%, 1/251494 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.78982e-06; MAF= 0.00088%, 1/113768 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00025% · 4 / 1,614,198
0 hom · FAF 7.9e-05%
European (non-Finnish)
4 / 1,180,042
0.00034%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0004% · 1 / 251,494
0 hom
European (non-Finnish)
1 / 113,768
0.00088%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 3297294)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.914. BayesDel score = 0.499098.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MYCL, a transcription factor, is altered by overexpression and amplification in various cancer types including small cell lung cancer.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots