VCV003257856.1 - ClinVar

NM_001291415.2(KDM6A):c.593dup (p.Asn198fs)

Germline

No data submitted for germline classification

Somatic

No data submitted for somatic clinical impact

Somatic

Oncogenicity

The aggregate oncogenicity classification for this variant for one or more tumor types, using the ClinGen/CGC/VICC terminology. 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 oncogenicity 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 oncogenic

criteria provided, single submitter

Variant Details

Identifiers

NM_001291415.2(KDM6A):c.593dup (p.Asn198fs)

Variation ID: 3257856 Accession: VCV003257856.1

Type and length

Duplication, 1 bp

Location

Cytogenetic: Xp11.3 X: 45034957-45034958 (GRCh38) [ NCBI UCSC ] X: 44894202-44894203 (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.
Somatic - Oncogenicity	Aug 11, 2024	Aug 11, 2024	Jul 31, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001291415.2:c.593dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001278344.1:p.Asn198fs	frameshift
NM_001291416.2:c.593dup	NP_001278345.1:p.Asn198fs	frameshift
NM_001291417.2:c.593dup	NP_001278346.1:p.Asn198fs	frameshift
NM_001291418.2:c.593dup	NP_001278347.1:p.Asn198fs	frameshift
NM_001291421.2:c.-161dup		5 prime UTR
NM_001410742.1:c.593dup	NP_001397671.1:p.Asn198fs	frameshift
NM_001419809.1:c.593dup	NP_001406738.1:p.Asn198fs	frameshift
NM_001419810.1:c.593dup	NP_001406739.1:p.Asn198fs	frameshift
NM_001419811.1:c.593dup	NP_001406740.1:p.Asn198fs	frameshift
NM_001419812.1:c.593dup	NP_001406741.1:p.Asn198fs	frameshift
NM_001419813.1:c.593dup	NP_001406742.1:p.Asn198fs	frameshift
NM_001419814.1:c.593dup	NP_001406743.1:p.Asn198fs	frameshift
NM_001419815.1:c.593dup	NP_001406744.1:p.Asn198fs	frameshift
NM_021140.4:c.593dup	NP_066963.2:p.Asn198fs	frameshift
NM_021140.4:c.593dupA		frameshift
NR_111960.2:n.957dup		non-coding transcript variant
NC_000023.11:g.45034959dup
NC_000023.10:g.44894204dup
NG_016260.1:g.166782dup
LRG_616:g.166782dup
LRG_616t1:c.593dup	LRG_616p1:p.Asn198Lysfs

... more HGVS ... less HGVS

Protein change

N198fs

Other names

Canonical SPDI

NC_000023.11:45034957:AA:AAA

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.
KDM6A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	977	1175

Conditions - Somatic

Tumor type Help The tumor type for this variant-condition (RCV) record in ClinVar.	Clinical impact (# of submissions) Help The aggregate somatic clinical impact for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to the aggregate somatic clinical impact is shown in parentheses. The corresponding review status for the RCV record is indicated by stars. Read our rules for calculating the review status.	Oncogenicity Help The aggregate oncogenicity classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to the aggregate oncogenicity classification is shown in parentheses. The corresponding review status for the RCV record is indicated by stars. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the tumor type.	Variation/condition record Help The most recent date that a submitter evaluated this variant for the tumor type.
Neoplasm		Likely oncogenic criteria provided, single submitter	Jul 31, 2024	RCV004666444.1

Submissions - Somatic

Oncogenicity Help The submitted oncogenicity 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)	Tumor type Help The tumor type 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 somatic clinical impact, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.

Likely oncogenic

(Jul 31, 2024)

(ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022)

Method: clinical testing

Neoplasm

Affected status: unknown

Allele origin: somatic

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Accession: SCV005094041.1
First In ClinVar: Aug 11, 2024
Last updated: Aug 11, 2024

Citations for somatic classification of this variant

There are no citations for somatic 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 Aug 11, 2024

ClinVar Genomic variation as it relates to human health

NM_001291415.2(KDM6A):c.593dup (p.Asn198fs)

Variant Details

Genes

Conditions - Somatic

Submissions - Somatic

Citations for somatic classification of this variant

Text-mined citations for this variant ...