VCV002574037.1 - ClinVar

NM_001987.5(ETV6):c.33+1G>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.

(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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001987.5(ETV6):c.33+1G>A

Variation ID: 2574037 Accession: VCV002574037.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 12p13.2 12: 11650161 (GRCh38) [ NCBI UCSC ] 12: 11803095 (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	Jul 29, 2023	Jul 29, 2023	Jul 25, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001987.5:c.33+1G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice donor
NM_001413913.1:c.33+1G>A		splice donor
NM_001413914.1:c.-120+1G>A		splice donor
NM_001413915.1:c.-102+1G>A		splice donor
NM_001413916.1:c.33+1G>A		splice donor
NM_001413917.1:c.33+1G>A		splice donor
NM_001413918.1:c.33+1G>A		splice donor
NC_000012.12:g.11650161G>A
NC_000012.11:g.11803095G>A
NG_011443.1:g.5308G>A
LRG_609:g.5308G>A

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000012.12:11650160: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.
ETV6		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	303	411

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.
Malignant lymphoma, large B-cell, diffuse	Likely pathogenic (1)	no assertion criteria provided	Jul 25, 2023	RCV003318466.1

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 (Jul 25, 2023)	no assertion criteria provided Method: clinical testing	Malignant lymphoma, large B-cell, diffuse (Somatic mutation) Affected status: yes Allele origin: somatic	Wasik Lab, Fox Chase Cancer Center Accession: SCV004020302.1 First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023	Publications: PubMed (1) PubMed: 35053500 Comment: This variant was observed in a patient with DLBCL that presented in leukemic form, best classified as MCD/C5 DLBCL, an ABC subtype. Despite an initial … (more) This variant was observed in a patient with DLBCL that presented in leukemic form, best classified as MCD/C5 DLBCL, an ABC subtype. Despite an initial good clinical response to BTK inhibitor ibrutinib, anti-CD20 antibody rituxan, alkylating agent bendamustine, and hematopoietic stem-cell transplant, the lymphoma relapsed, accompanied by morphologic and molecular evidence of disease progression. ETV6 is a transcription factor with a critical role in hematopoiesis and embryonic development, frequently mutated in hematologic malignancies. ETV6 c.33+1G>A was present at initial presentation, but was not detected in relapsed tumor. This variant changes a consensus splice donor site and is expected to affect protein structure. Although alterations in ETV6 are one of the hallmark features of the MCD/C5 group, its oncogenic role in DLBCL remains undefined (Marino et al. 2022). (less) Indication for testing: DLBCL Age: 50-59 years Sex: female Comment on evidence: Peripheral blood containing DLBCL collected for sequencing at initial diagnosis August 2018. Tumor tissue sequenced at recurrence September 2019. Testing laboratory: Genoptix Date variant was reported to submitter: 2019-10-10 Testing laboratory interpretation: Pathogenic

Comment:

This variant was observed in a patient with DLBCL that presented in leukemic form, best classified as MCD/C5 DLBCL, an ABC subtype. Despite an initial good clinical response to BTK inhibitor ibrutinib, anti-CD20 antibody rituxan, alkylating agent bendamustine, and hematopoietic stem-cell transplant, the lymphoma relapsed, accompanied by morphologic and molecular evidence of disease progression. ETV6 is a transcription factor with a critical role in hematopoiesis and embryonic development, frequently mutated in hematologic malignancies. ETV6 c.33+1G>A was present at initial presentation, but was not detected in relapsed tumor. This variant changes a consensus splice donor site and is expected to affect protein structure. Although alterations in ETV6 are one of the hallmark features of the MCD/C5 group, its oncogenic role in DLBCL remains undefined (Marino et al. 2022).

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

Title	Author	Journal	Year	Link
High ETV6 Levels Support Aggressive B Lymphoma Cell Survival and Predict Poor Outcome in Diffuse Large B-Cell Lymphoma Patients.	Marino D	Cancers	2022	PMID: 35053500

Text-mined citations for this variant ...

Record last updated Aug 06, 2023

ClinVar Genomic variation as it relates to human health

NM_001987.5(ETV6):c.33+1G>A

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...