NM_001122740.1:c.970C>A

ESR1 · NP_001116212.1:p.(Pro324Thr) · NM_001122740.1

GRCh37: chr6:152265517 C>A · GRCh38: chr6:151944382 C>A

Gene: ESR1 Transcript: NM_001122740.1

Final call

VUS

PM2 supporting PP3 supporting

Variant details

Gene

ESR1

Transcript

NM_001122740.1

Protein

NP_001116212.1:p.(Pro324Thr)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_001122740.1:c.970C>A (p.Pro324Thr) is a missense variant in exon 5 of ESR1.

This variant is absent from gnomAD population databases (v2.1, v4.1, and gnomAD-Canada), meeting PM2 at supporting strength.

Computational evidence supports a deleterious effect: REVEL score 0.844 (damaging) and BayesDel noAF score 0.302 (above the -0.36 damaging threshold), meeting PP3 at supporting strength.

No ClinVar entries exist for this variant; no functional studies, segregation data, or case-control data are available.

PVS1 is not applicable: this is a missense variant that does not meet null-variant criteria per PMC6185798.

With only two supporting pathogenic criteria (PM2, PP3) and no benign criteria met, this variant is classified as a Variant of Uncertain Significance (VUS) per generic ACMG/AMP 2015 combination rules (PMID:25741868).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	This variant is a missense substitution (c.970C>A, p.Pro324Thr) and does not fall into the ClinGen SVI PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	No known pathogenic variant causing the same amino acid change (Pro324Thr) via a different nucleotide substitution has been identified in ClinVar or the literature.	clinvar
PS2	Not met	No de novo observation with confirmed paternity and maternity is available for this variant.
PS3	Not met	No functional studies directly testing NM_001122740.1:c.970C>A (p.Pro324Thr) or a systematically characterized range including residue 324 were identified. OncoKB reports Unknown Oncogenic Effect. Computational prediction alone (REVEL 0.844) does not satisfy PS3 experimental evidence requirements.	oncokb
PS4	Not met	No case-control or prevalence data comparing affected individuals to controls is available for this variant.
PS5	Not met	No alternate pathogenic variant at the same residue (Pro324) has been identified in ClinVar or the literature to support PS5.	clinvar
PM1	Not met	Residue Pro324 is not located in a statistically significant cancer hotspot per cancerhotspots.org. Although ESR1 position 324 lies within the ligand-binding domain (aa 302–552), no domain-level functional evidence was identified in the case materials to support PM1 application per generic ACMG 2015 criteria.
PM2	Met	This variant is absent from all gnomAD population databases (v2.1 exomes, v4.1 exomes, and gnomAD-Canada v1.0 genomes), meeting the PM2 threshold of <0.1% allele frequency.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No pathogenic missense variant at the same amino acid residue (Pro324) was identified for comparison. Automated PM5 candidate harvesting returned zero candidates.	pm5_candidates clinvar
PM6	Not met	No de novo observation (without confirmation of paternity and maternity) is available for this variant.
PP1	Not met	No co-segregation data with disease in multiple affected family members is available for this variant.
PP2	Not met	Insufficient data to establish that ESR1 has a low rate of benign missense variation with missense variants as a common disease mechanism. gnomAD missense constraint metrics (Z-score) are not available in the case materials.
PP3	Met	Multiple lines of in silico computational evidence support a deleterious effect. REVEL score of 0.844 falls well above the damaging threshold (>0.5). BayesDel noAF score of 0.302 is above the -0.36 damaging threshold, providing additional in silico support. SpliceAI predicts no splicing impact (max delta 0.00).	revel bayesdel spliceai
PP4	Not met	No patient phenotype or family history data specific to the disease gene was provided for assessment.
PP5	Not met	This variant is absent from ClinVar and no reputable source (including 3-star expert panel) has classified it as pathogenic.	clinvar
BA1	Not met	This variant is absent from all gnomAD population databases; allele frequency of 0% does not exceed the BA1 threshold of >1%.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	This variant is absent from all gnomAD population databases; allele frequency of 0% does not exceed the BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No data on homozygous or hemizygous observations of this variant in healthy adults are available.
BS3	Not met	No functional studies demonstrating a neutral or benign effect for NM_001122740.1:c.970C>A (p.Pro324Thr) were identified.
BS4	Not met	No segregation data in affected family members demonstrating lack of co-segregation with disease is available.
BP1	Not met	ESR1 is not a gene where only truncating variants cause disease. Published evidence (PMID:41129222) suggests rare regulatory and potentially coding alleles of ESR1 may contribute to inherited breast cancer predisposition, indicating missense variants may be disease-relevant.
BP2	Not met	No data on observation of this variant in trans with a known pathogenic dominant variant are available.
BP4	Not met	Multiple lines of computational evidence do not support a benign impact. REVEL score of 0.844 and BayesDel score of 0.302 both predict a deleterious effect. SpliceAI predicts no splicing impact (max delta 0.00) but this alone does not outweigh the damaging missense predictions.	revel bayesdel spliceai
BP5	Not met	No data demonstrating that this variant is consistently absent in individuals with ESR1-related disease are available.
BP6	Not met	This variant is absent from ClinVar and no reputable source (including 3-star expert panel) has classified it as benign.	clinvar
BP7	N/A	This variant is a missense substitution (c.970C>A, p.Pro324Thr), not a synonymous variant; BP7 applies exclusively to synonymous variants with no predicted splice impact.

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