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.1 The variant is absent from ClinVar; no clinical laboratory or expert panel classification exists.2 No functional studies, de novo observations, segregation data, case-control comparisons, or literature citations mentioning this specific variant were identified.3 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.4 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.5 PVS1 does not apply (missense variant); PM5 does not apply (no same-residue comparator variants identified).6 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.7 This variant is classified as a Variant of Uncertain Significance (VUS).
ESR1
Final classification
VUS
ESR1 c.1661G>A · p.Ser554Asn
ESR1
NM_001122740.1:c.1661G>A (p.Ser554Asn) is a missense variant in exon 9 of ESR1 encoding estrogen receptor alpha.
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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2
VUS
ESR1 c.1661G>A
PM2
→
VUS
3
oncokb ↗
4
revelbayesdelspliceai ↗
5
oncokb ↗
6
pvs1_variant_assessmentpm5_candidates
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 · 1 applied · 21 assessed
Applied · 1
Strength
Supporting
Moderate
Strong
Very strong
✓
PM2
supporting
Pathogenic
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 v2.1: AF=7.07e-06 (2/2827620 hom)
Assessed · not applied
Pathogenic
PS1
No known pathogenic variant with a different amino acid change at the same position (Ser554) has been reported in ClinVar or the literature.
PS2
No de novo observation with confirmed maternity and paternity has been reported for this variant in the literature or ClinVar.
PS3
No experimental functional studies testing this exact variant or a systematically characterized range that includes residue 554 were identified.
PS4
No case-control or cohort prevalence data are available to assess enrichment of this variant in affected individuals versus controls.
PM1
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.
PM6
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.
PP1
No co-segregation data are available for this variant in affected families.
PP2
ESR1 is not recognized as a gene where missense variants are a well-established predominant mechanism of germline disease.
PP3
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).
PP4
No clinical phenotype information for the proband is available; cannot assess specificity of presentation for ESR1-related disease.
PP5
The variant is absent from ClinVar; no reputable clinical laboratory or expert panel has classified this variant as pathogenic.
Benign
BA1
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.
BS1
The highest population allele frequency is 0.005% (gnomAD v2.1 East Asian), below the 0.3% BS1 threshold for a strong benign criterion.
BS2
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).
BS3
No well-established in vitro or in vivo functional studies have been identified that demonstrate no damaging effect for this variant.
BS4
No segregation or non-segregation data are available for this variant.
BP1
ESR1 is not a gene where predominantly truncating variants are established as the sole cause of germline disease.
BP2
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.
BP4
In silico evidence is mixed and does not reach the consensus required for BP4.
BP5
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
The variant is absent from ClinVar; no reputable source has classified it as benign.
N/A · 4
PVS1 · PM5 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.85867e-06; MAF= 0.00019%, 3/1614058 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 4.45673e-05; MAF= 0.00446%, 2/44876 alleles, homozygotes = 0); grpmax FAF= 7.39e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 7.07309e-06; MAF= 0.00071%, 2/282762 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 5.01153e-05; MAF= 0.00501%, 1/19954 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00019%
· 3 / 1,614,058
0 hom · FAF 0.00074%
0 hom · FAF 0.00074%
East Asian 2 / 44,876 |
0.0045% |
European (non-Finnish) 1 / 1,180,034 |
8.5e-05% |
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.00071%
· 2 / 282,762
0 hom
0 hom
East Asian 1 / 19,954 |
0.005% |
European (non-Finnish) 1 / 129,082 |
0.00077% |
+ 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.213. BayesDel score = -0.538498.
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.
COSMIC
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