VCV002431576.1 - ClinVar

NM_207037.2(TCF12):c.1621_1622del (p.Glu541fs)

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.

(1)

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.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_207037.2(TCF12):c.1621_1622del (p.Glu541fs)

Variation ID: 2431576 Accession: VCV002431576.1

Type and length

Deletion, 2 bp

Location

Cytogenetic: 15q21.3 15: 57263149-57263150 (GRCh38) [ NCBI UCSC ] 15: 57555347-57555348 (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	Mar 5, 2023	Mar 4, 2023	May 31, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_207037.2:c.1621_1622del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_996920.1:p.Glu541fs	frameshift
NM_001306219.3:c.1111_1112del	NP_001293148.1:p.Glu371fs	frameshift
NM_001306220.3:c.841_842del	NP_001293149.1:p.Glu281fs	frameshift
NM_001322151.2:c.1621_1622del	NP_001309080.1:p.Glu541fs	frameshift
NM_001322152.2:c.1621_1622del	NP_001309081.1:p.Glu541fs	frameshift
NM_001322154.2:c.964_965del	NP_001309083.1:p.Glu322fs	frameshift
NM_001322156.2:c.1447_1448del	NP_001309085.1:p.Glu483fs	frameshift
NM_001322157.3:c.1549_1550del	NP_001309086.1:p.Glu517fs	frameshift
NM_001322158.2:c.1375_1376del	NP_001309087.1:p.Glu459fs	frameshift
NM_001322159.3:c.1621_1622del	NP_001309088.1:p.Glu541fs	frameshift
NM_001322161.2:c.1618_1619del	NP_001309090.1:p.Glu540fs	frameshift
NM_001322162.2:c.1621_1622del	NP_001309091.1:p.Glu541fs	frameshift
NM_001322164.2:c.1585_1586del	NP_001309093.1:p.Glu529fs	frameshift
NM_001322165.2:c.1549_1550del	NP_001309094.1:p.Glu517fs	frameshift
NM_003205.4:c.1549_1550del	NP_003196.1:p.Glu517fs	frameshift
NM_207036.2:c.1621_1622del	NP_996919.1:p.Glu541fs	frameshift
NM_207038.2:c.1549_1550del	NP_996921.1:p.Glu517fs	frameshift
NM_207040.2:c.1039_1040del	NP_996923.1:p.Glu347fs	frameshift
NC_000015.10:g.57263150_57263151del
NC_000015.9:g.57555348_57555349del
NG_033851.2:g.350061_350062del

... more HGVS ... less HGVS

Protein change

E281fs, E322fs, E347fs, E371fs, E459fs, E483fs, E517fs, E529fs, E540fs, E541fs

Other names

Canonical SPDI

NC_000015.10:57263148:AGA: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.
Hypogonadotropic hypogonadism 26 with or without anosmia	Likely pathogenic (1)	criteria provided, single submitter	May 31, 2022	RCV003140630.1

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 (May 31, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Hypogonadotropic hypogonadism 26 with or without anosmia Affected status: yes Allele origin: germline	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein Accession: SCV003807588.1 First in ClinVar: Mar 04, 2023 Last updated: Mar 04, 2023	Comment: ACMG classification criteria: PVS1 very strong, PM2 moderated Number of individuals with the variant: 1 Clinical Features: Hypogonadotropic hypogonadism (present) , Increased body weight (present) , Hyposmia (present) Geographic origin: Brazil Method: Paired-end whole-genome sequencing

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.

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 Mar 11, 2023

ClinVar Genomic variation as it relates to human health

NM_207037.2(TCF12):c.1621_1622del (p.Glu541fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...