VCV002034271.3 - ClinVar

NM_207037.2(TCF12):c.1036-6G>A

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_207037.2(TCF12):c.1036-6G>A

Variation ID: 2034271 Accession: VCV002034271.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 15q21.3 15: 57243466 (GRCh38) [ NCBI UCSC ] 15: 57535664 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 8, 2023	Feb 20, 2024	Jul 7, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_207037.2:c.1036-6G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		intron variant
NM_001306219.3:c.526-6G>A		intron variant
NM_001306220.3:c.328-6G>A		intron variant
NM_001322151.2:c.1036-6G>A		intron variant
NM_001322152.2:c.1036-6G>A		intron variant
NM_001322154.2:c.379-6G>A		intron variant
NM_001322156.2:c.862-6G>A		intron variant
NM_001322157.3:c.1036-6G>A		intron variant
NM_001322158.2:c.862-6G>A		intron variant
NM_001322159.3:c.1036-6G>A		intron variant
NM_001322161.2:c.1036-6G>A		intron variant
NM_001322162.2:c.1036-6G>A		intron variant
NM_001322164.2:c.1072-6G>A		intron variant
NM_001322165.2:c.1036-6G>A		intron variant
NM_003205.4:c.1036-6G>A		intron variant
NM_207036.2:c.1036-6G>A		intron variant
NM_207038.2:c.1036-6G>A		intron variant
NM_207040.2:c.526-6G>A		intron variant
NC_000015.10:g.57243466G>A
NC_000015.9:g.57535664G>A
NG_033851.2:g.330377G>A

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000015.10:57243465:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
TCF12		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	380	402

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Uncertain significance (1)	criteria provided, single submitter	Jul 7, 2023	RCV002885407.3
TCF12-related craniosynostosis	Likely pathogenic (1)	criteria provided, single submitter	-	RCV003319998.4

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	TCF12-related craniosynostosis (Autosomal dominant inheritance) Affected status: yes Allele origin: de novo	HUSP Clinical Genetics Laboratory, Hospital Universitario San Pedro De Logroño (HUSP) Accession: SCV004024227.1 First in ClinVar: Aug 13, 2023 Last updated: Aug 13, 2023 Comment: The variant was detected in a 5-years-old girl with craniosynostosis and strabismus . The c.1036-6G>A variant in the 12 intron of the TCF12 gene (NM_207037.2) … (more) The variant was detected in a 5-years-old girl with craniosynostosis and strabismus . The c.1036-6G>A variant in the 12 intron of the TCF12 gene (NM_207037.2) is predicted to change the canonical splicing. This variant is not detected in general population. Pathogenic variants in the TCF12 gene have been associated with the following phenotype: craniosynostosis (OMIM:615314), with autosomal dominant inheritance. A genetic study has been carried out in the parents and it is determined that none of them presents the variant, so it appears de novo in our patient. (less)	Number of individuals with the variant: 1 Clinical Features: Craniosynostosis syndrome (present) , Strabismus (present)
Uncertain significance (Jul 07, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003239163.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024	Comment: This sequence change falls in intron 12 of the TCF12 gene. It does not directly change the encoded amino acid sequence of the TCF12 protein. … (more) This sequence change falls in intron 12 of the TCF12 gene. It does not directly change the encoded amino acid sequence of the TCF12 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TCF12-related conditions. ClinVar contains an entry for this variant (Variation ID: 2034271). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)

Comment:

This sequence change falls in intron 12 of the TCF12 gene. It does not directly change the encoded amino acid sequence of the TCF12 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TCF12-related conditions. ClinVar contains an entry for this variant (Variation ID: 2034271). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_207037.2(TCF12):c.1036-6G>A

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...