NM_000128.3(F11):c.1481-1G>T AND Hereditary factor XI deficiency disease

Clinical significance:Conflicting interpretations of pathogenicity, Likely pathogenic(1);Uncertain significance(1) (Last evaluated: Dec 5, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000412477.2

Allele description [Variation Report for NM_000128.3(F11):c.1481-1G>T]

NM_000128.3(F11):c.1481-1G>T

Genes:
F11-AS1:F11 antisense RNA 1 [Gene - HGNC]
F11:coagulation factor XI [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4q35.2
Genomic location:
Preferred name:
NM_000128.3(F11):c.1481-1G>T
HGVS:
  • NC_000004.12:g.186286414G>T
  • NG_008051.1:g.25451G>T
  • NM_000128.3:c.1481-1G>T
  • LRG_583t1:c.1481-1G>T
  • LRG_583:g.25451G>T
  • NC_000004.11:g.187207568G>T
Links:
dbSNP: rs1057516506
NCBI 1000 Genomes Browser:
rs1057516506
Molecular consequence:
  • NM_000128.3:c.1481-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Hereditary factor XI deficiency disease
Synonyms:
Plasma thromboplastin antecedent deficiency; PTA deficiency; F11 deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012897; MedGen: C0015523; Orphanet: 329; OMIM: 612416

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000485791Counsylcriteria provided, single submitter
Likely pathogenic
(Feb 12, 2016)
unknownclinical testing

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf,

Citation Link,

SCV000916057Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Dec 5, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Counsyl, SCV000485791.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Clinical Services Laboratory,Illumina, SCV000916057.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The F11 c.1481-1G>T variant occurs in a canonical splice site (acceptor) and is therefore predicted to disrupt or distort the normal gene product. It was observed by ICSL 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 for this variant, it could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene and cDNA change. No publications were found based on this search. Due to the potential impact of splice acceptor variants and the lack of clarifying evidence, this variant is classified as a variant of uncertain significance but suspicious for pathogenicity for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 7, 2021

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