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ERBB4
Final classification
VUS
ERBB4 c.2371A>G · p.Thr791Ala
ERBB4

NM_005235.2:c.2371A>G (p.Thr791Ala) is a missense variant in exon 20 of ERBB4. It is present at extremely low frequency in population databases (gnomAD v2.1: 3/251,416 alleles, AF=0.00119%; gnomAD v4.1: 24/1,614,034 alleles, AF=0.00149%) with no homozygotes observed, meeting PM2 at supporting strength.

Gene
ERBB4
Transcript
NM_005235.2
HGVS · transcript:coding
NM_005235.2:c.2371A>G
Consequence
N/A
GRCh38
chr2:211562019 T>C
GRCh37
chr2:212426744 T>C
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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, 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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
ERBB4 c.2371A>G

NM_005235.2:c.2371A>G (p.Thr791Ala) is a missense variant in exon 20 of ERBB4. It is present at extremely low frequency in population databases (gnomAD v2.1: 3/251,416 alleles, AF=0.00119%; gnomAD v4.1: 24/1,614,034 alleles, AF=0.00149%) with no homozygotes observed, meeting PM2 at supporting strength.1 Multiple computational predictors support a benign interpretation: REVEL score of 0.321 is below the pathogenic threshold, BayesDel score of -0.090 is in the benign range, and SpliceAI predicts no splice impact (max delta = 0.00). BP4 is met at supporting strength.2 This variant has been reported in ClinVar as Uncertain significance by two clinical laboratories (LabCorp, Ambry Genetics), each with criteria provided as a single submitter. No expert panel review has been performed.3 No functional studies, segregation data, de novo observations, case-control studies, or family co-segregation data are available for this variant. The variant lies within the ERBB4 kinase domain but is not located in a recognized mutational hotspot.4 Applying the generic ACMG/AMP 2015 final classification rules (PMID:25741868): one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) result in an overall classification of Uncertain Significance. The evidence is balanced and insufficient to classify this variant as either likely pathogenic or likely benign.5

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_005235.2 · variants mapped to exon structure
ERBB4 NM_005235.2
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
      This variant is present in gnomAD v4.1 (AF= 1.48696e-05; MAF= 0.00149%, 24/1614034 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 8.00747e-05; MAF= 0.00801%, 6/74930 alleles, homozygotes = 0); grpmax FAF= 3.471e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.19324e-05; MAF= 0.00119%, 3/251416 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.63764e-05; MAF= 0.00264%, 3/113738 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0015% · 24 / 1,614,034
      0 hom · FAF 0.0035%
      African/African American
      6 / 74,930
      0.008%
      European (non-Finnish)
      18 / 1,180,036
      0.0015%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0012% · 3 / 251,416
      0 hom · FAF 0.0007%
      European (non-Finnish)
      3 / 113,738
      0.0026%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 3063763)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.321. BayesDel score = -0.0903471.
      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. ERBB4, a receptor tyrosine kinase, is altered at low to moderate frequencies in various cancer types, most frequently in melanoma and lung cancer.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 12 PMIDs not cited in assessment
      23619275 ↗ ACMG position statement on prenatal/preconception expanded carrier screening. CLINVAR
      23652378 ↗ A framework to start the debate on neonatal screening policies in the EU: an Expert Opinion Document. CLINVAR
      25626707 ↗ Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. CLINVAR
      25730230 ↗ Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. CLINVAR
      23169492 ↗ The perspective from EASAC and FEAM on direct-to-consumer genetic testing for health-related purposes. CLINVAR
      24121147 ↗ Appropriateness of newborn screening for α1-antitrypsin deficiency. CLINVAR
      22947299 ↗ Specific guidelines for assessing and improving the methodological quality of economic evaluations of newborn screening. CLINVAR
      23037933 ↗ Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children. CLINVAR
      23881473 ↗ Newborn screening: education, consent, and the residual blood spot. The position of the national society of genetic counselors. CLINVAR
      24022298 ↗ Offering prenatal diagnostic tests: European guidelines for clinical practice [corrected]. CLINVAR
      24394680 ↗ Parental permission for pilot newborn screening research: guidelines from the NBSTRN. CLINVAR
      31022120 ↗ ACOG Committee Opinion No. 778 Summary: Newborn Screening and the Role of the Obstetrician-Gynecologist. CLINVAR