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ESR1
Final classification
VUS
ESR1 c.1150C>G · p.Leu384Val
ESR1

NM_001122740.1:c.1150C>G (p.Leu384Val) is a missense variant in ESR1 exon 6. It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 across all populations (PM2_Supporting).

Gene
ESR1
Transcript
NM_001122740.1
HGVS · transcript:coding
NM_001122740.1:c.1150C>G
Consequence
N/A
GRCh38
chr6:152011709 C>G
GRCh37
chr6:152332844 C>G
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: PM2 supporting, PP3 supporting; combination = 2 supporting, 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: PM2 supporting, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
ESR1 c.1150C>G

NM_001122740.1:c.1150C>G (p.Leu384Val) is a missense variant in ESR1 exon 6. It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 across all populations (PM2_Supporting).1 Multiple in silico predictors support a deleterious effect: REVEL score 0.863 and BayesDel score 0.279 both exceed their respective pathogenicity thresholds (PP3_Supporting).2 The variant is absent from ClinVar, COSMIC, and all population databases. No functional studies, case reports, cosegregation data, or de novo observations exist for this variant.3 PVS1 is not applicable as this is a missense variant that does not fall into the null-variant buckets per ClinGen SVI PVS1 recommendations (PMC6185798).4 This variant does not lie in a statistically significant mutational hotspot (cancerhotspots.org negative), and no pathogenic ClinVar variants cluster at residue Leu384. PM1 is not met.5 No publications were identified that mention NM_001122740.1:c.1150C>G. A targeted review of five ESR1 germline disease-context publications (PMID:15361840, PMID:25139996, PMID:41129222, PMID:22086303, PMID:26557847) confirmed none contain variant-specific evidence. Overall classification: Variant of Uncertain Significance (VUS). Two supporting-level pathogenic criteria (PM2_Supporting, PP3_Supporting) are met, which is insufficient to reach Likely Pathogenic under the generic ACMG/AMP 2015 classification rules (PMID:25741868). No benign criteria are met.6

PM2 + PP3 VUS
Gene diagram · NM_001122740.1 · variants mapped to exon structure
ESR1 NM_001122740.1
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_001122740.1:c.1150C>G is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 across all populations. This satisfies the generic ACMG/AMP PM2 threshold of <0.1% allele frequency in population databases.
Absent from gnomAD v2.1 (exomes)v4.1 (exomes)and gnomAD-Canada v1.0 (genomes).
PP3 supporting Pathogenic
Multiple in silico predictors support a deleterious effect. REVEL score is 0.863 (above the 0.75 threshold for pathogenicity). BayesDel score is 0.279 (above the 0.27 damaging threshold). SpliceAI max delta is 0.00, which is expected for a missense variant without predicted splice effect. The concordance of protein-level predictors supports PP3 at supporting level.
REVEL 0.863 (deleterious)BayesDel 0.279 (damaging)SpliceAI max delta 0.00 (no splice effect
Assessed · not applied
Pathogenic
PS1 No alternative nucleotide change at the same amino acid position (Leu384) with a pathogenic classification has been identified.
PS2 No de novo occurrence data are available for this variant.
PS3 No functional studies have been identified for this variant.
PS4 No case-control or cohort studies have reported this variant.
PM1 This variant (p.Leu384Val) lies within the ESR1 ligand-binding domain (aa ~302-552), a well-characterized functional domain.
PM6 No de novo occurrence has been reported for this variant.
PP1 No cosegregation data are available.
PP2 PP2 requires demonstration that the gene has a low rate of benign missense variation and that missense variants are a common disease mechanism.
PP4 No patient phenotype or family history data are available.
PP5 No reputable source has reported this variant as pathogenic.
Benign
BA1 The variant is absent from all gnomAD populations (v2.1, v4.1, Canada v1.0).
BS1 The variant is absent from all gnomAD populations.
BS2 No data are available showing observation of this variant in a healthy adult for a recessive disorder, or in trans with a pathogenic variant for a dominant disorder.
BS3 No well-established functional studies demonstrate a benign effect for this variant.
BS4 No segregation data are available for this variant.
BP1 BP1 applies when a missense variant occurs in a gene where primarily truncating variants cause disease.
BP2 No data are available showing observation of this variant in trans with a pathogenic variant for a dominant disorder, or in cis with a pathogenic variant.
BP4 BP4 requires multiple lines of computational evidence suggesting no impact.
BP5 No evidence is available showing this variant in a case with an alternate molecular basis for disease.
BP6 No reputable source has reported this variant as benign.
N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · BP7
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 = 0.00). REVEL score = 0.863. BayesDel score = 0.278555.
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 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