VCV002577994.1 - ClinVar

NM_022893.4(BCL11A):c.1616_1619del (p.Glu539fs)

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_022893.4(BCL11A):c.1616_1619del (p.Glu539fs)

Variation ID: 2577994 Accession: VCV002577994.1

Type and length

Deletion, 4 bp

Location

Cytogenetic: 2p16.1 2: 60461293-60461296 (GRCh38) [ NCBI UCSC ] 2: 60688428-60688431 (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	Sep 3, 2023	Sep 3, 2023	May 25, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NM_022893.4:c.1616_1619del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_075044.2:p.Glu539fs	frameshift
NM_001363864.1:c.1514_1517del	NP_001350793.1:p.Glu505fs	frameshift
NM_001365609.1:c.1514_1517del	NP_001352538.1:p.Glu505fs	frameshift
NM_001405708.1:c.1616_1619del	NP_001392637.1:p.Glu539fs	frameshift
NM_001405709.1:c.1616_1619del	NP_001392638.1:p.Glu539fs	frameshift
NM_001405710.1:c.1616_1619del	NP_001392639.1:p.Glu539fs	frameshift
NM_001405711.1:c.1514_1517del	NP_001392640.1:p.Glu505fs	frameshift
NM_001405712.1:c.1514_1517del	NP_001392641.1:p.Glu505fs	frameshift
NM_001405713.1:c.1460_1463del	NP_001392642.1:p.Glu487fs	frameshift
NM_001405714.1:c.1460_1463del	NP_001392643.1:p.Glu487fs	frameshift
NM_001405715.1:c.1460_1463del	NP_001392644.1:p.Glu487fs	frameshift
NM_001405716.1:c.1460_1463del	NP_001392645.1:p.Glu487fs	frameshift
NM_001405717.1:c.1358_1361del	NP_001392646.1:p.Glu453fs	frameshift
NM_001405718.1:c.1358_1361del	NP_001392647.1:p.Glu453fs	frameshift
NM_001405719.1:c.1514_1517del	NP_001392648.1:p.Glu505fs	frameshift
NM_001405720.1:c.1283_1286del	NP_001392649.1:p.Glu428fs	frameshift
NM_001405721.1:c.1283_1286del	NP_001392650.1:p.Glu428fs	frameshift
NM_001405722.1:c.1460_1463del	NP_001392651.1:p.Glu487fs	frameshift
NM_001405723.1:c.1460_1463del	NP_001392652.1:p.Glu487fs	frameshift
NM_001405724.1:c.1358_1361del	NP_001392653.1:p.Glu453fs	frameshift
NM_001405725.1:c.1160_1163del	NP_001392654.1:p.Glu387fs	frameshift
NM_001405726.1:c.1160_1163del	NP_001392655.1:p.Glu387fs	frameshift
NM_001405727.1:c.1160_1163del	NP_001392656.1:p.Glu387fs	frameshift
NM_001405728.1:c.1160_1163del	NP_001392657.1:p.Glu387fs	frameshift
NM_001405729.1:c.923_926del	NP_001392658.1:p.Glu308fs	frameshift
NM_001405730.1:c.1079_1082del	NP_001392659.1:p.Glu360fs	frameshift
NM_001405731.1:c.623_626del	NP_001392660.1:p.Glu208fs	frameshift
NM_001405732.1:c.630+986_630+989del		intron variant
NM_001405733.1:c.528+986_528+989del		intron variant
NM_001405734.1:c.474+986_474+989del		intron variant
NM_001405735.1:c.474+986_474+989del		intron variant
NM_001405736.1:c.372+986_372+989del		intron variant
NM_018014.4:c.1616_1619del	NP_060484.2:p.Glu539fs	frameshift
NM_138559.2:c.630+986_630+989del		intron variant
NC_000002.12:g.60461294_60461297del
NC_000002.11:g.60688429_60688432del
NG_011968.1:g.97203_97206del

... more HGVS ... less HGVS

Protein change

E208fs, E308fs, E360fs, E387fs, E428fs, E453fs, E487fs, E505fs, E539fs

Other names

Canonical SPDI

NC_000002.12:60461292:CTCTC:C

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.
BCL11A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	237	264

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	Likely pathogenic (1)	no assertion criteria provided	May 25, 2021	RCV003325400.2

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 25, 2021)	no assertion criteria provided Method: clinical testing	not provided Affected status: yes Allele origin: de novo	Molecular Genetics laboratory, Necker Hospital Accession: SCV004031397.1 First in ClinVar: Sep 03, 2023 Last updated: Sep 03, 2023	Clinical Features: Intellectual disability (present)

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 Sep 01, 2024

ClinVar Genomic variation as it relates to human health

NM_022893.4(BCL11A):c.1616_1619del (p.Glu539fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...