VCV000690430.2 - ClinVar

NM_001165963.4(SCN1A):c.2616_3206delinsAAGTTGGCAAAA (p.Trp873_Ile1069delinsSerTrpGlnAsn)

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_001165963.4(SCN1A):c.2616_3206delinsAAGTTGGCAAAA (p.Trp873_Ile1069delinsSerTrpGlnAsn)

Variation ID: 690430 Accession: VCV000690430.2

Type and length

Indel, 1,836 bp

Location

Cytogenetic: 2q24.3 2: 166892781-166894616 (GRCh37) [ NCBI UCSC ] 2: 166036271-166038106 (GRCh38) [ 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 28, 2019	Sep 28, 2019	Mar 16, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NM_001165963.4:c.2616_3206delinsAAGTTGGCAAAA MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001159435.1:p.Trp873_Ile1069delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001165964.3:c.2532_3122delinsAAGTTGGCAAAA	NP_001159436.1:p.Trp845_Ile1041delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001202435.3:c.2616_3206delinsAAGTTGGCAAAA	NP_001189364.1:p.Trp873_Ile1069delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353948.2:c.2616_3206delinsAAGTTGGCAAAA	NP_001340877.1:p.Trp873_Ile1069delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353949.2:c.2583_3173delinsAAGTTGGCAAAA	NP_001340878.1:p.Trp862_Ile1058delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353950.2:c.2583_3173delinsAAGTTGGCAAAA	NP_001340879.1:p.Trp862_Ile1058delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353951.2:c.2583_3173delinsAAGTTGGCAAAA	NP_001340880.1:p.Trp862_Ile1058delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353952.2:c.2583_3173delinsAAGTTGGCAAAA	NP_001340881.1:p.Trp862_Ile1058delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353954.2:c.2580_3170delinsAAGTTGGCAAAA	NP_001340883.1:p.Trp861_Ile1057delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353955.2:c.2580_3170delinsAAGTTGGCAAAA	NP_001340884.1:p.Trp861_Ile1057delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353957.2:c.2532_3122delinsAAGTTGGCAAAA	NP_001340886.1:p.Trp845_Ile1041delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353958.2:c.2532_3122delinsAAGTTGGCAAAA	NP_001340887.1:p.Trp845_Ile1041delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353960.2:c.2529_3119delinsAAGTTGGCAAAA	NP_001340889.1:p.Trp844_Ile1040delinsSerTrpGlnAsn	splice acceptor splice donor
NM_001353961.2:c.174_764delinsAAGTTGGCAAAA	NP_001340890.1:p.Trp59_Ile255delinsSerTrpGlnAsn	splice acceptor splice donor
NM_006920.6:c.2583_3173delinsAAGTTGGCAAAA	NP_008851.3:p.Trp862_Ile1058delinsSerTrpGlnAsn	splice acceptor splice donor
NR_148667.2:n.2969_3559delinsAAGTTGGCAAAA		splice acceptor splice donor non-coding transcript variant
NC_000002.12:g.166036271_166038106delinsTTTTGCCAACTT
NC_000002.11:g.166892781_166894616delinsTTTTGCCAACTT
NG_011906.1:g.40534_42369delinsAAGTTGGCAAAA
LRG_8:g.40534_42369delinsAAGTTGGCAAAA

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

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.
SCN1A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	2241	4627
LOC102724058	-	-	-	GRCh38	-	2327

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.
Generalized epilepsy with febrile seizures plus, type 2	Pathogenic (1)	criteria provided, single submitter	Mar 16, 2018	RCV000851368.2

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.
Pathogenic (Mar 16, 2018)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Generalized epilepsy with febrile seizures plus, type 2 (Autosomal dominant inheritance) Affected status: yes Allele origin: de novo	Undiagnosed Diseases Network, NIH Study: Undiagnosed Diseases Network (NIH), UDN Accession: SCV000993584.1 First in ClinVar: Sep 28, 2019 Last updated: Sep 28, 2019	Number of individuals with the variant: 1 Clinical Features: Synophrys (present) , Seizures (present) , Scoliosis (present) , Numerous nevi (present) , Micrognathia (present) , Impulsivity (present) , Global developmental delay (present) , Attention … (more) Synophrys (present) , Seizures (present) , Scoliosis (present) , Numerous nevi (present) , Micrognathia (present) , Impulsivity (present) , Global developmental delay (present) , Attention deficit hyperactivity disorder (present) (less) Age: 10-19 years Sex: female Ethnicity/Population group: Iranian, Sephardic Jewish Tissue: blood

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 Aug 16, 2022

ClinVar Genomic variation as it relates to human health

NM_001165963.4(SCN1A):c.2616_3206delinsAAGTTGGCAAAA (p.Trp873_Ile1069delinsSerTrpGlnAsn)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...