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RET
Final classification
Likely Pathogenic
RET c.2434del · p.Leu812CysfsTer57
RET

NM_020975.5:c.2434del is a frameshift variant in exon 14 of 20, predicted to cause a premature termination codon (p.Leu812CysfsTer57) and trigger nonsense-mediated decay.

Gene
RET
Transcript
NM_020975.5
HGVS · transcript:coding
NM_020975.5:c.2434del
Consequence
N/A
GRCh38
chr10:43119569 TC>T
GRCh37
chr10:43615017 TC>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
RET c.2434del

NM_020975.5:c.2434del is a frameshift variant in exon 14 of 20, predicted to cause a premature termination codon (p.Leu812CysfsTer57) and trigger nonsense-mediated decay.1 RET loss-of-function is an established disease mechanism for Hirschsprung disease, meeting PVS1 at very strong strength under ClinGen SVI PVS1 recommendations (PMC6185798).2 The variant truncates the RET tyrosine kinase domain (aa 724-1016) at codon 868, removing the activation loop and C-terminal tail. This domain is a critical functional domain characterized in the literature, meeting PM1 at moderate strength. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting PM2 at moderate strength under generic ACMG allele frequency thresholds.3 No pathogenic benign criteria are met. The variant is absent from ClinVar, has no functional studies, and lacks segregation or case-control data.4 Under generic ACMG/AMP 2015 combination rules (Richards et al. 2015), 1 very strong criterion (PVS1) plus 2 moderate criteria (PM1, PM2) meets the threshold for Pathogenic classification.5

PVS1 + PM2 Likely Pathogenic
1 pvs1_variant_assessmentpvs1_generic_framework ↗
2 pvs1_gene_context
5 generic_acmg_combination_rules
Gene diagram · NM_020975.5 · variants mapped to exon structure
RET NM_020975.5
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
NM_020975.5:c.2434del is a frameshift variant in exon 14 of 20, predicted to produce a premature termination codon at position 868 (p.Leu812CysfsTer57) and trigger nonsense-mediated decay. RET loss-of-function is an established mechanism for Hirschsprung disease. Under ClinGen PVS1 recommendations (PMC6185798), this null variant qualifies for PVS1 at very strong strength.
Frameshift at c.2434 in exon 14 of 20 exonspredicted to trigger NMDRET loss-of-function is an established disease mechanism for Hirschsprung disease
PM2 moderate Pathogenic
NM_020975.5:c.2434del is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. Under generic ACMG rules, PM2 applies at moderate strength for variants with allele frequency below 0.1% in all population databases.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes)Absent from gnomAD-Canada v1.0
Assessed · not applied
Pathogenic
PS2 No de novo observation has been reported for NM_020975.5:c.2434del.
PS3 No functional studies have been performed on NM_020975.5:c.2434del or on a systematically characterized range that includes codon 812.
PS4 No case-control or prevalence data are available for this variant.
PM1 The variant occurs at codon 812 within the RET tyrosine kinase domain (aa 724-1016), a well-characterized critical functional domain.
PM6 No de novo observation has been reported for NM_020975.5:c.2434del.
PP1 No segregation data are available for NM_020975.5:c.2434del.
PP3 SpliceAI predicts no splice impact (max delta score = 0.00).
PP4 No patient phenotype or clinical data are available for this case.
PP5 NM_020975.5:c.2434del is absent from ClinVar.
Benign
BA1 NM_020975.5:c.2434del is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
BS1 NM_020975.5:c.2434del is absent from all gnomAD population databases.
BS2 No observations in healthy adults are documented for NM_020975.5:c.2434del.
BS3 No functional studies demonstrating a neutral or benign effect are available for NM_020975.5:c.2434del.
BS4 No segregation data are available for assessment of lack of segregation with disease.
BP2 No data on observation in trans with a known pathogenic variant are available for NM_020975.5:c.2434del.
BP4 SpliceAI predicts no splice impact (max delta score = 0.00), but this does not constitute multiple lines of computational evidence suggesting a benign effect.
BP5 No observation of NM_020975.5:c.2434del in a case with an alternate molecular basis for disease has been documented.
BP6 NM_020975.5:c.2434del is absent from ClinVar.
N/A · 7 PS1 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
Research & evidence
Population frequency · supports pathogenic
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
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