VCV003148668.1 - ClinVar

NM_000546.6(TP53):c.838_851delinsTGACCAAAT (p.Arg280_Thr284delinsTer)

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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000546.6(TP53):c.838_851delinsTGACCAAAT (p.Arg280_Thr284delinsTer)

Variation ID: 3148668 Accession: VCV003148668.1

Type and length

Indel, 14 bp

Location

Cytogenetic: 17p13.1 17: 7673769-7673782 (GRCh38) [ NCBI UCSC ] 17: 7577087-7577100 (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	May 1, 2024	May 1, 2024	Jan 10, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_000546.6:c.838_851delinsTGACCAAAT MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000537.3:p.Arg280_Thr284delinsTer	nonsense
NM_001126112.3:c.838_851delinsTGACCAAAT	NP_001119584.1:p.Arg280_Thr284delinsTer	nonsense
NM_001126113.3:c.838_851delinsTGACCAAAT	NP_001119585.1:p.Arg280_Thr284delinsTer	nonsense
NM_001126114.3:c.838_851delinsTGACCAAAT	NP_001119586.1:p.Arg280_Thr284delinsTer	nonsense
NM_001126115.2:c.442_455delinsTGACCAAAT	NP_001119587.1:p.Arg148_Thr152delinsTer	nonsense
NM_001126116.2:c.442_455delinsTGACCAAAT	NP_001119588.1:p.Arg148_Thr152delinsTer	nonsense
NM_001126117.2:c.442_455delinsTGACCAAAT	NP_001119589.1:p.Arg148_Thr152delinsTer	nonsense
NM_001126118.2:c.721_734delinsTGACCAAAT	NP_001119590.1:p.Arg241_Thr245delinsTer	nonsense
NM_001276695.3:c.721_734delinsTGACCAAAT	NP_001263624.1:p.Arg241_Thr245delinsTer	nonsense
NM_001276696.3:c.721_734delinsTGACCAAAT	NP_001263625.1:p.Arg241_Thr245delinsTer	nonsense
NM_001276697.3:c.361_374delinsTGACCAAAT	NP_001263626.1:p.Arg121_Thr125delinsTer	nonsense
NM_001276698.3:c.361_374delinsTGACCAAAT	NP_001263627.1:p.Arg121_Thr125delinsTer	nonsense
NM_001276699.3:c.361_374delinsTGACCAAAT	NP_001263628.1:p.Arg121_Thr125delinsTer	nonsense
NM_001276760.3:c.721_734delinsTGACCAAAT	NP_001263689.1:p.Arg241_Thr245delinsTer	nonsense
NM_001276761.3:c.721_734delinsTGACCAAAT	NP_001263690.1:p.Arg241_Thr245delinsTer	nonsense
NM_001407262.1:c.838_851delinsTGACCAAAT	NP_001394191.1:p.Arg280_Thr284delinsTer	nonsense
NM_001407263.1:c.721_734delinsTGACCAAAT	NP_001394192.1:p.Arg241_Thr245delinsTer	nonsense
NM_001407264.1:c.838_851delinsTGACCAAAT	NP_001394193.1:p.Arg280_Thr284delinsTer	nonsense
NM_001407265.1:c.721_734delinsTGACCAAAT	NP_001394194.1:p.Arg241_Thr245delinsTer	nonsense
NM_001407266.1:c.838_851delinsTGACCAAAT	NP_001394195.1:p.Arg280_Thr284delinsTer	nonsense
NM_001407267.1:c.721_734delinsTGACCAAAT	NP_001394196.1:p.Arg241_Thr245delinsTer	nonsense
NM_001407268.1:c.838_851delinsTGACCAAAT	NP_001394197.1:p.Arg280_Thr284delinsTer	nonsense
NM_001407269.1:c.721_734delinsTGACCAAAT	NP_001394198.1:p.Arg241_Thr245delinsTer	nonsense
NM_001407270.1:c.838_851delinsTGACCAAAT	NP_001394199.1:p.Arg280_Thr284delinsTer	nonsense
NM_001407271.1:c.721_734delinsTGACCAAAT	NP_001394200.1:p.Arg241_Thr245delinsTer	nonsense
NR_176326.1:n.867_880delinsTGACCAAAT		non-coding transcript variant
NC_000017.11:g.7673769_7673782delinsATTTGGTCA
NC_000017.10:g.7577087_7577100delinsATTTGGTCA
NG_017013.2:g.18769_18782delinsTGACCAAAT
LRG_321:g.18769_18782delinsTGACCAAAT
LRG_321t1:c.838_851delAGAGACCGGCGCACinsTGACCAAAT	LRG_321p1:p.Arg280Terfs
LRG_321t2:c.838_851delAGAGACCGGCGCACinsTGACCAAAT	LRG_321:p.Arg280Terfs
LRG_321t3:c.838_851delAGAGACCGGCGCACinsTGACCAAAT	LRG_321p3:p.Arg280Terfs
LRG_321t4:c.838_851delAGAGACCGGCGCACinsTGACCAAAT	LRG_321p4:p.Arg280Terfs
LRG_321t5:c.442_455delAGAGACCGGCGCACinsTGACCAAAT	LRG_321p5:p.Arg148Terfs
LRG_321t6:c.442_455delAGAGACCGGCGCACinsTGACCAAAT	LRG_321p6:p.Arg148Terfs
LRG_321t7:c.442_455delAGAGACCGGCGCACinsTGACCAAAT	LRG_321p7:p.Arg148Terfs
LRG_321t8:c.721_734delAGAGACCGGCGCACinsTGACCAAAT	LRG_321p8:p.Arg241Terfs

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000017.11:7673768:GTGCGCCGGTCTCT:ATTTGGTCA

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.
TP53		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	3373	3472

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.
Li-Fraumeni syndrome 1	Pathogenic (1)	criteria provided, single submitter	Jan 10, 2024	RCV004442562.1

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.
Pathogenic (Jan 10, 2024)	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023)) Method: clinical testing	Li-Fraumeni syndrome 1 Affected status: unknown Allele origin: unknown	Myriad Genetics, Inc. Accession: SCV004930857.1 First in ClinVar: May 01, 2024 Last updated: May 01, 2024	Comment: This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.

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 May 08, 2024

ClinVar Genomic variation as it relates to human health

NM_000546.6(TP53):c.838_851delinsTGACCAAAT (p.Arg280_Thr284delinsTer)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...