Starting
Initialising…
0%
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
      Population frequency
      Overall AF
      24 / 1,614,034
      0.0015%
      Highest · African/African American
      0.008%
      Homozygotes
      0
      grpmax FAF
      0.0035%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 2 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      African/African American 6 / 74,930 0.008% 0
      European (non-Finnish) 18 / 1,180,036 0.0015% 0
      Admixed American 0 / 59,994
      European (Finnish) 0 / 64,018
      Amish 0 / 912
      East Asian 0 / 44,884
      Middle Eastern 0 / 6,076
      South Asian 0 / 91,090
      Ashkenazi Jewish 0 / 29,608
      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.
      Overall AF
      3 / 251,416
      0.0012%
      Highest · European (non-Finnish)
      0.0026%
      Homozygotes
      0
      grpmax FAF
      0.0007%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 1 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 3 / 113,738 0.0026% 0
      African/African American 0 / 16,254
      Admixed American 0 / 34,584
      Ashkenazi Jewish 0 / 10,078
      East Asian 0 / 18,392
      European (Finnish) 0 / 21,616
      Remaining individuals 0 / 6,138
      South Asian 0 / 30,616
      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.
      This variant is absent from gnomAD-Canada.
      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.
      Literature · 12 PMIDs triaged · 6 high-priority
      12papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      23619275 ↗ splicing rna
      ACMG position statement on prenatal/preconception expanded carrier screening.
      For years, clinicians have offered gene-by-gene carrier screening to patients and couples considering future pregnancy or those with an ongoing pregnancy early in gestation. Examples include ethnic-specific screening offered to Ashkenazi Jewish patients and panethnic screening for cystic fibrosis and spinal muscular atrophy. Next-generation sequencing methods now available permit screening for man
      BP7PP3PP5PS4PVS1
      23652378 ↗ splicing rna
      A framework to start the debate on neonatal screening policies in the EU: an Expert Opinion Document.
      The European Union (EU) Council Recommendation on rare diseases urged the member states to implement national and EU collaborative actions to improve the health care of rare disease patients. Following this recommendation, the European Commission launched a tender on newborn screening (NBS) to report on current practices of laboratory testing, form a network of experts and provide guidance on how
      BP7PP3PP5PS4PVS1
      25626707 ↗ splicing rna
      Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes.
      The advent and refinement of sequencing technologies has resulted in a decrease in both the cost and time needed to generate data on the entire sequence of the human genome. This has increased the accessibility of using whole-genome sequencing and whole-exome sequencing approaches for analysis in both the research and clinical contexts. The expectation is that more services based on these and othe
      BP7PP3PP5PS4PVS1
      25730230 ↗ splicing rna
      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.
      The Perinatal Quality Foundation and the American College of Medical Genetics and Genomics, in association with the American College of Obstetricians and Gynecologists, the Society for Maternal-Fetal Medicine, and the National Society of Genetic Counselors, have collaborated to provide education for clinicians and laboratories regarding the use of expanded genetic carrier screening in reproductive
      BP7PP3PP5PS4PVS1
      23169492 ↗ case observation
      The perspective from EASAC and FEAM on direct-to-consumer genetic testing for health-related purposes.
      Direct-to-consumer (DTC) genetic testing services raise scientific, regulatory and ethical questions. A report was prepared by consultation with an expert Working Group and published by the academies of science (European Academies of Science Advisory Council, EASAC) and medicine (Federation of European Academies of Medicine, FEAM). This report reviews current scientific evidence, ascertains the pr
      PP5PS4
      24121147 ↗ case observation
      Appropriateness of newborn screening for α1-antitrypsin deficiency.
      The Alpha-1 Foundation convened a workshop to consider the appropriateness of newborn screening for α-1-antitrypsin (AAT) deficiency. A review of natural history and technical data was conducted. Homozygous ZZ AAT deficiency is a common genetic disease occurring in 1 in 2000 to 3500 births; however, it is underrecognized and most patients are undiagnosed. AAT deficiency can cause chronic liv
      PP5PS4
      22947299 ↗ background review
      Specific guidelines for assessing and improving the methodological quality of economic evaluations of newborn screening.
      PP5PS4
      23037933 ↗ background review
      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.
      PP5PS4
      23881473 ↗ background review
      Newborn screening: education, consent, and the residual blood spot. The position of the national society of genetic counselors.
      PP5PS4
      24022298 ↗ background review
      Offering prenatal diagnostic tests: European guidelines for clinical practice [corrected].
      PP5PS4
      24394680 ↗ background review
      Parental permission for pilot newborn screening research: guidelines from the NBSTRN.
      PP5PS4
      31022120 ↗ background review
      ACOG Committee Opinion No. 778 Summary: Newborn Screening and the Role of the Obstetrician-Gynecologist.
      PP5PS4
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots