NM_001122740.1:c.1661G>A

ESR1 · NP_001116212.1:p.(Ser554Asn) · NM_001122740.1

GRCh37: chr6:152419974 G>A · GRCh38: chr6:152098839 G>A

Gene: ESR1 Transcript: NM_001122740.1

Final call

VUS

PM2 supporting

Variant details

Gene

ESR1

Transcript

NM_001122740.1

Protein

NP_001116212.1:p.(Ser554Asn)

gnomAD AF

1.8586692671514902e-06 (v4.1)

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_001122740.1:c.1661G>A (p.Ser554Asn) is a missense variant in exon 9 of ESR1 encoding estrogen receptor alpha.

The variant is extremely rare in population databases: gnomAD v2.1 allele frequency 7.07×10⁻⁶ (2/282,762 alleles) and gnomAD v4.1 allele frequency 1.86×10⁻⁶ (3/1,614,058 alleles), both well below the 0.1% threshold for PM2 at supporting strength.

The variant is absent from ClinVar; no clinical laboratory or expert panel classification exists.

No functional studies, de novo observations, segregation data, case-control comparisons, or literature citations mentioning this specific variant were identified.

In silico predictors are mixed: BayesDel (−0.538) predicts benign, SpliceAI (max delta 0.0) predicts no splicing alteration, and REVEL (0.213) is in the indeterminate range.

Residue 554 lies C-terminal to the ligand-binding domain (LBD, aa ~302–552) and is not within a known critical functional domain or statistically significant mutational hotspot.

PVS1 does not apply (missense variant); PM5 does not apply (no same-residue comparator variants identified).

The only applicable criterion is PM2 at supporting strength. Per ACMG/AMP 2015 classification rules (PMID:25741868), a single supporting pathogenic criterion without any other evidence is insufficient for classification as likely pathogenic or pathogenic.

This variant is classified as a Variant of Uncertain Significance (VUS).

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	Missense variant (p.Ser554Asn); PVS1 applies only to null variants (nonsense, frameshift, canonical splice ±1,2). Per ClinGen SVI PVS1 recommendations (PMC6185798), this variant does not fall into any eligible null-variant bucket.	pvs1_generic_framework pvs1_variant_assessment pvs1_gene_context
PS1	Not met	No known pathogenic variant with a different amino acid change at the same position (Ser554) has been reported in ClinVar or the literature.	clinvar pm5_candidates
PS2	Not met	No de novo observation with confirmed maternity and paternity has been reported for this variant in the literature or ClinVar.	clinvar
PS3	Not met	No experimental functional studies testing this exact variant or a systematically characterized range that includes residue 554 were identified. OncoKB reports 'Unknown Oncogenic Effect.' In silico predictors (REVEL 0.213, BayesDel −0.538) do not support a damaging functional effect.	oncokb revel bayesdel
PS4	Not assessed	No case-control or cohort prevalence data are available to assess enrichment of this variant in affected individuals versus controls.
PS5	Not assessed	No alternative variant at nucleotide position c.1661 with a different alternate allele has been classified as pathogenic in ClinVar.	clinvar
PM1	Not met	Residue 554 lies C-terminal to the ESR1 ligand-binding domain (LBD, residues ~302–552) and AF-2 activation helix (helix 12, ~535–552); it is not within a known critical functional domain. Neither the residue nor the exact variant is a statistically significant mutational hotspot (cancerhotspots.org).	oncokb
PM2	Met	This variant is extremely rare in population databases: gnomAD v2.1 allele frequency 7.07×10⁻⁶ (2/282,762 alleles), gnomAD v4.1 allele frequency 1.86×10⁻⁶ (3/1,614,058 alleles), grpmax FAF 7.39×10⁻⁶. All frequencies are well below the 0.1% PM2 threshold. Absent from gnomAD-Canada.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	Unable to confirm classic same-residue PM5 semantics; no comparator variant at residue 554 with a different alternate amino acid and pathogenic classification was identified.	pm5_candidates
PM6	Not met	No de novo observation has been reported for this variant in the literature or ClinVar; PM6 requires confirmed de novo status with maternity/paternity testing.	clinvar
PP1	Not met	No co-segregation data are available for this variant in affected families.
PP2	Not met	ESR1 is not recognized as a gene where missense variants are a well-established predominant mechanism of germline disease. While somatic missense mutations in ESR1 are well-described in hormone-resistant breast cancer, the gene lacks a well-characterized germline disease spectrum meeting PP2 criteria.	oncokb pvs1_gene_context
PP3	Not met	In silico tools do not support a deleterious effect: REVEL score 0.213 is in the indeterminate range (threshold for pathogenicity >0.5), BayesDel score −0.538 is negative (predicts benign), and SpliceAI max delta score is 0.0 (no predicted splicing impact). No HCI prior score is available for ESR1.	revel bayesdel spliceai
PP4	Not assessed	No clinical phenotype information for the proband is available; cannot assess specificity of presentation for ESR1-related disease.
PP5	Not met	The variant is absent from ClinVar; no reputable clinical laboratory or expert panel has classified this variant as pathogenic. PP5 requires a classification from a source with supporting-level credibility (ClinVar 1-star submitter or higher).	clinvar
BA1	Not met	The highest population allele frequency observed is 5.01×10⁻⁵ (0.005%, East Asian gnomAD v2.1), well below the 1% BA1 threshold for a stand-alone benign classification.	gnomad_v2
BS1	Not met	The highest population allele frequency is 0.005% (gnomAD v2.1 East Asian), below the 0.3% BS1 threshold for a strong benign criterion.	gnomad_v2 gnomad_v4
BS2	Not met	Only 2–3 alleles have been observed in gnomAD across all populations (total alleles surveyed: 282,762 in v2.1 and 1,614,058 in v4.1). This is insufficient observation in healthy adults to meet BS2, which requires the variant to be observed in multiple healthy individuals in a manner consistent with benign impact.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established in vitro or in vivo functional studies have been identified that demonstrate no damaging effect for this variant. OncoKB lists 'Unknown Oncogenic Effect' and no variant-specific functional data.	oncokb
BS4	Not assessed	No segregation or non-segregation data are available for this variant.
BP1	Not met	ESR1 is not a gene where predominantly truncating variants are established as the sole cause of germline disease. The PVS1 gene context identifies literature supporting LOF mechanism but no well-characterized germline syndrome where missense variants can be dismissed via BP1.	pvs1_gene_context
BP2	Not met	No observation of this variant in trans with a pathogenic variant for a recessive disorder, or in cis with a pathogenic variant for a dominant disorder, has been reported.
BP3	N/A	Skipped: variant is a substitution, not an in-frame indel in a repetitive region.
BP4	Not met	In silico evidence is mixed and does not reach the consensus required for BP4. BayesDel predicts benign (−0.538) and SpliceAI shows no splicing impact (max delta 0.0), but REVEL (0.213) is indeterminate. The evidence does not meet the 'multiple lines of computational evidence suggesting no impact' standard.	revel bayesdel spliceai
BP5	Not met	No case has been identified in which this variant is present in a patient with an alternate molecular basis for disease (i.e., a co-occurring pathogenic variant explaining the phenotype).
BP6	Not met	The variant is absent from ClinVar; no reputable source has classified it as benign. BP6 requires a classification from a source with supporting-level credibility.	clinvar
BP7	N/A	BP7 applies to synonymous variants with no predicted splicing impact. This variant is missense (p.Ser554Asn), not synonymous.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.