NM_001372051.1(CASP8):c.339C>T (p.Ser113=) AND Autoimmune lymphoproliferative syndrome type 2B
- Germline classification:
- Benign/Likely benign (2 submissions)
- Last evaluated:
- Jan 31, 2024
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000293283.13
Allele description [Variation Report for NM_001372051.1(CASP8):c.339C>T (p.Ser113=)]
NM_001372051.1(CASP8):c.339C>T (p.Ser113=)
- Gene:
- CASP8:caspase 8 [Gene - OMIM - HGNC]
- Variant type:
- single nucleotide variant
- Cytogenetic location:
- 2q33.1
- Genomic location:
- Preferred name:
- NM_001372051.1(CASP8):c.339C>T (p.Ser113=)
- HGVS:
- NC_000002.12:g.201271549C>T
- NG_007497.1:g.43092C>T
- NM_001080124.2:c.339C>T
- NM_001080125.2:c.516C>T
- NM_001228.5:c.435C>T
- NM_001372051.1:c.339C>TMANE SELECT
- NM_001400642.1:c.516C>T
- NM_001400645.1:c.339C>T
- NM_001400648.1:c.339C>T
- NM_001400651.1:c.339C>T
- NM_001400653.1:c.339C>T
- NM_001400654.1:c.339C>T
- NM_001400655.1:c.339C>T
- NM_001400656.1:c.339C>T
- NM_001400657.1:c.339C>T
- NM_001400658.1:c.339C>T
- NM_001400659.1:c.339C>T
- NM_001400660.1:c.339C>T
- NM_001400661.1:c.339C>T
- NM_001400662.1:c.339C>T
- NM_001400663.1:c.339C>T
- NM_001400664.1:c.339C>T
- NM_001400665.1:c.516C>T
- NM_001400666.1:c.339C>T
- NM_001400667.1:c.339C>T
- NM_001400668.1:c.339C>T
- NM_001400669.1:c.30C>T
- NM_001400670.1:c.339C>T
- NM_001400671.1:c.-194C>T
- NM_001400672.1:c.-194C>T
- NM_001400673.1:c.-194C>T
- NM_001400674.1:c.-375C>T
- NM_001400675.1:c.-194C>T
- NM_001400676.1:c.-194C>T
- NM_001400677.1:c.-194C>T
- NM_001400678.1:c.-194C>T
- NM_001400679.1:c.339C>T
- NM_001400680.1:c.-273C>T
- NM_001400750.1:c.-194C>T
- NM_001400751.1:c.-194C>T
- NM_033355.4:c.339C>T
- NM_033356.4:c.339C>T
- NP_001073593.1:p.Ser113=
- NP_001073594.1:p.Ser172=
- NP_001219.2:p.Ser145=
- NP_001219.2:p.Ser145=
- NP_001358980.1:p.Ser113=
- NP_001387571.1:p.Ser172=
- NP_001387574.1:p.Ser113=
- NP_001387577.1:p.Ser113=
- NP_001387580.1:p.Ser113=
- NP_001387582.1:p.Ser113=
- NP_001387583.1:p.Ser113=
- NP_001387584.1:p.Ser113=
- NP_001387585.1:p.Ser113=
- NP_001387586.1:p.Ser113=
- NP_001387587.1:p.Ser113=
- NP_001387588.1:p.Ser113=
- NP_001387589.1:p.Ser113=
- NP_001387590.1:p.Ser113=
- NP_001387591.1:p.Ser113=
- NP_001387592.1:p.Ser113=
- NP_001387593.1:p.Ser113=
- NP_001387594.1:p.Ser172=
- NP_001387595.1:p.Ser113=
- NP_001387596.1:p.Ser113=
- NP_001387597.1:p.Ser113=
- NP_001387598.1:p.Ser10=
- NP_001387599.1:p.Ser113=
- NP_001387608.1:p.Ser113=
- NP_203519.1:p.Ser113=
- NP_203519.1:p.Ser113=
- NP_203520.1:p.Ser113=
- LRG_34t1:c.435C>T
- LRG_34t2:c.339C>T
- LRG_34t3:c.339C>T
- LRG_34:g.43092C>T
- LRG_34p1:p.Ser145=
- LRG_34p2:p.Ser113=
- LRG_34p3:p.Ser113=
- NC_000002.11:g.202136272C>T
- NM_001228.4:c.435C>T
- NM_033355.3:c.339C>T
- NR_111983.2:n.713C>T
- NR_174583.1:n.554C>T
- NR_174584.1:n.713C>T
- NR_174585.1:n.485C>T
- NR_174586.1:n.459C>T
- NR_174588.1:n.622C>T
- NR_174589.1:n.417C>T
- NR_174590.1:n.554C>T
- NR_174591.1:n.485C>T
- NR_174592.1:n.687C>T
- NR_174593.1:n.485C>T
- NR_174594.1:n.528C>T
- NR_174595.1:n.443C>T
- NR_174596.1:n.443C>T
- NR_174597.1:n.443C>T
- NR_174598.1:n.622C>T
- NR_174599.1:n.443C>T
- NR_174600.1:n.713C>T
- NR_174601.1:n.459C>T
- NR_174602.1:n.443C>T
This HGVS expression did not pass validation- Links:
- dbSNP: rs17860422
- NCBI 1000 Genomes Browser:
- rs17860422
- Molecular consequence:
- NM_001400671.1:c.-194C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400672.1:c.-194C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400673.1:c.-194C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400674.1:c.-375C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400675.1:c.-194C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400676.1:c.-194C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400677.1:c.-194C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400678.1:c.-194C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400680.1:c.-273C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400750.1:c.-194C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NM_001400751.1:c.-194C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
- NR_111983.2:n.713C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174583.1:n.554C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174584.1:n.713C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174585.1:n.485C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174586.1:n.459C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174588.1:n.622C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174589.1:n.417C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174590.1:n.554C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174591.1:n.485C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174592.1:n.687C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174593.1:n.485C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174594.1:n.528C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174595.1:n.443C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174596.1:n.443C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174598.1:n.622C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174599.1:n.443C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174600.1:n.713C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174601.1:n.459C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_174602.1:n.443C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NM_001080124.2:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001080125.2:c.516C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001228.5:c.435C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001372051.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400642.1:c.516C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400645.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400648.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400651.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400653.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400654.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400655.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400656.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400657.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400658.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400659.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400660.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400661.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400662.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400663.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400664.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400665.1:c.516C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400666.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400667.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400668.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400669.1:c.30C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400670.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_001400679.1:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_033355.4:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
- NM_033356.4:c.339C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Condition(s)
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000426172 | Illumina Laboratory Services, Illumina | criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) | Likely benign (Jan 13, 2018) | germline | clinical testing | |
SCV000762579 | Labcorp Genetics (formerly Invitae), Labcorp | criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) | Benign (Jan 31, 2024) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
Citations
PubMed
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.
Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.
- PMID:
- 28492532
- PMCID:
- PMC5632818
Details of each submission
From Illumina Laboratory Services, Illumina, SCV000426172.3
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
Description
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Labcorp Genetics (formerly Invitae), Labcorp, SCV000762579.6
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: Sep 29, 2024