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ESR1
Final classification
VUS
ESR1 c.1235G>A · p.Arg412Lys
ESR1

This missense variant (c.1235G>A, p.Arg412Lys) lies within the ESR1 ligand-binding domain (LBD, residues 305–552), a critical functional domain required for estrogen binding and receptor transactivation (PM1).

Gene
ESR1
Transcript
NM_001122740.1
HGVS · transcript:coding
NM_001122740.1:c.1235G>A
Consequence
N/A
GRCh38
chr6:152011794 G>A
GRCh37
chr6:152332929 G>A
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: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PM1PM2 VUS
ESR1 c.1235G>A

This missense variant (c.1235G>A, p.Arg412Lys) lies within the ESR1 ligand-binding domain (LBD, residues 305–552), a critical functional domain required for estrogen binding and receptor transactivation (PM1).1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0, with an allele frequency of 0% across all populations (PM2).2 No functional studies assessing the effect of p.Arg412Lys on ESR1 activity were identified; PS3 is not met.3 Computational evidence is inconsistent: REVEL score 0.487 is borderline, BayesDel score 0.300 is indeterminate, and SpliceAI predicts no splicing impact (max delta 0.01); PP3 is not met and BP4 is not met.4 The variant is absent from ClinVar, with no pathogenic or benign assertions from any submitter; PS5, PP5, and BP6 are not met.5 No published literature reporting this specific variant was identified; PS1, PS2, PS3, PS4, PM6, PP1, and PP4 could not be assessed due to absence of variant-specific clinical or functional data. With only PM1 (moderate) and PM2 (moderate) met, the variant does not reach the Likely Pathogenic threshold per generic ACMG/AMP 2015 combination rules (PMID:25741868), which require at least 3 moderate criteria or 1 strong criterion for Likely Pathogenic.6 This variant is classified as a Variant of Uncertain Significance (VUS) per generic ACMG/AMP 2015 framework.7

PM1 + PM2 VUS
4 revelbayesdelspliceai ↗
6 generic_acmg_combination_rules
7 generic_acmg_combination_rules
Gene diagram · NM_001122740.1 · variants mapped to exon structure
ESR1 NM_001122740.1
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      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 = 0.01). REVEL score = 0.487. BayesDel score = 0.299838.
      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. ESR1 (estrogen receptor alpha) is a transcription factor that is frequently mutated in hormone-resistant metastatic breast cancers.
      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 previously been reported in somatic cancers (COSMIC; COSV105067291, n = 1 times).
      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