VCV002575555.1 - ClinVar

NM_001190737.2(NFIB):c.1057_1059del (p.Ser353del)

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.

Uncertain significance

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001190737.2(NFIB):c.1057_1059del (p.Ser353del)

Variation ID: 2575555 Accession: VCV002575555.1

Type and length

Deletion, 3 bp

Location

Cytogenetic: 9p23 9: 14125633-14125635 (GRCh38) [ NCBI UCSC ] 9: 14125632-14125634 (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	Aug 19, 2023	Aug 19, 2023	Feb 13, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001190737.2:c.1057_1059del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001177666.1:p.Ser353del	inframe deletion
NM_001190738.2:c.1135_1137del	NP_001177667.1:p.Ser379del	inframe deletion
NM_001282787.2:c.301_303del	NP_001269716.1:p.Ser101del	inframe deletion
NM_001369458.1:c.1123_1125del	NP_001356387.1:p.Ser375del	inframe deletion
NM_001369459.1:c.1123_1125del	NP_001356388.1:p.Ser375del	inframe deletion
NM_001369460.1:c.1045_1047del	NP_001356389.1:p.Ser349del	inframe deletion
NM_001369461.1:c.1057_1059del	NP_001356390.1:p.Ser353del	inframe deletion
NM_001369462.1:c.1123_1125del	NP_001356391.1:p.Ser375del	inframe deletion
NM_001369463.1:c.1045_1047del	NP_001356392.1:p.Ser349del	inframe deletion
NM_001369464.1:c.1057_1059del	NP_001356393.1:p.Ser353del	inframe deletion
NM_001369465.1:c.1030_1032del	NP_001356394.1:p.Ser344del	inframe deletion
NM_001369466.1:c.1045_1047del	NP_001356395.1:p.Ser349del	inframe deletion
NM_001369467.1:c.1030_1032del	NP_001356396.1:p.Ser344del	inframe deletion
NM_001369468.1:c.1123_1125del	NP_001356397.1:p.Ser375del	inframe deletion
NM_001369469.1:c.913_915del	NP_001356398.1:p.Ser305del	inframe deletion
NM_001369470.1:c.820_822del	NP_001356399.1:p.Ser274del	inframe deletion
NM_001369471.1:c.1057_1057+2del		splice donor
NM_001369472.1:c.1045_1047del	NP_001356401.1:p.Ser349del	inframe deletion
NM_001369473.1:c.1045_1045+2del		splice donor
NM_001369474.1:c.1042_1042+2del		splice donor
NM_001369475.1:c.832_834del	NP_001356404.1:p.Ser278del	inframe deletion
NM_001369476.1:c.1030_1032del	NP_001356405.1:p.Ser344del	inframe deletion
NM_001369477.1:c.1003_1003+2del		splice donor
NM_001369478.1:c.820_822del	NP_001356407.1:p.Ser274del	inframe deletion
NM_001369479.1:c.520_522del	NP_001356408.1:p.Ser174del	inframe deletion
NM_001369480.1:c.520_522del	NP_001356409.1:p.Ser174del	inframe deletion
NM_005596.3:c.1057_1059del	NP_005587.2:p.Ser353del	inframe deletion
NR_161382.1:n.591_593del		non-coding transcript variant
NR_161384.1:n.589_591del		non-coding transcript variant
NR_161385.1:n.641_643del		non-coding transcript variant
NC_000009.12:g.14125633_14125635del
NC_000009.11:g.14125632_14125634del

... more HGVS ... less HGVS

Protein change

S101del, S174del, S274del, S278del, S305del, S344del, S349del, S353del, S375del, S379del

Other names

Canonical SPDI

NC_000009.12:14125632:ACT:

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.
NFIB		-	-	GRCh38 GRCh37	132	259

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	Uncertain significance (1)	criteria provided, single submitter	Feb 13, 2023	RCV003321121.1

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.
Uncertain significance (Feb 13, 2023)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV004025280.1 First in ClinVar: Aug 19, 2023 Last updated: Aug 19, 2023	Comment: Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of one amino acid in a non-repeat region; In silico analysis supports a … (more) Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of one amino acid in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge (less)

Comment:

Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of one amino acid in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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

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 19, 2023

ClinVar Genomic variation as it relates to human health

NM_001190737.2(NFIB):c.1057_1059del (p.Ser353del)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...