VCV002675653.3 - ClinVar

NM_001113378.2(FANCI):c.3116del (p.Tyr1039fs)

Germline

Classification

criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.

Pathogenic/Likely pathogenic

2 out of 2 submissions contributed to this 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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001113378.2(FANCI):c.3116del (p.Tyr1039fs)

Variation ID: 2675653 Accession: VCV002675653.3

Type and length

Deletion, 1 bp

Location

Cytogenetic: 15q26.1 15: 89305172 (GRCh38) [ NCBI UCSC ] 15: 89848403 (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	Dec 30, 2023	Mar 4, 2025	Mar 29, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001113378.2:c.3116del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001106849.1:p.Tyr1039fs	frameshift
NM_001376910.1:c.2837del	NP_001363839.1:p.Tyr946fs	frameshift
NM_001376911.1:c.3116del	NP_001363840.1:p.Tyr1039fs	frameshift
NM_018193.3:c.2936del	NP_060663.2:p.Tyr979fs	frameshift
NC_000015.10:g.89305172del
NC_000015.9:g.89848403del
NG_008218.2:g.34624del
NG_011736.1:g.66210del
NG_160687.1:g.115del
LRG_500:g.66210del
LRG_500t1:c.3116del	LRG_500p1:p.Tyr1039Leufs
LRG_765:g.34624del

... more HGVS ... less HGVS

Protein change

Y1039fs, Y946fs, Y979fs

Other names

Canonical SPDI

NC_000015.10:89305171: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

ClinGen: CA7723597 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.
FANCI		-	-	GRCh38 GRCh37	2240	2448

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.
Fanconi anemia complementation group I	Likely pathogenic (1)	criteria provided, single submitter	May 10, 2022	RCV003468180.1
Fanconi anemia	Pathogenic (1)	criteria provided, single submitter	Mar 29, 2023	RCV003523189.3

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 10, 2022) C Contributing to aggregate classification	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Fanconi anemia complementation group I Affected status: unknown Allele origin: unknown	Baylor Genetics Accession: SCV004197246.1 First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023
Pathogenic (Mar 29, 2023) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Fanconi anemia Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004294790.2 First in ClinVar: Feb 14, 2024 Last updated: Mar 04, 2025	Publications: PubMed (2) PubMed: 17452773‚ 17460694 Comment: This sequence change creates a premature translational stop signal (p.Tyr1039Leufs22) in the FANCI gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.Tyr1039Leufs22) in the FANCI gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCI are known to be pathogenic (PMID: 17452773, 17460694). This variant is present in population databases (rs772733800, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with FANCI-related conditions. For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

This sequence change creates a premature translational stop signal (p.Tyr1039Leufs*22) in the FANCI gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FANCI are known to be pathogenic (PMID: 17452773, 17460694). This variant is present in population databases (rs772733800, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with FANCI-related conditions. For these reasons, this variant has been classified as Pathogenic.

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
FANCI is a second monoubiquitinated member of the Fanconi anemia pathway.	Sims AE	Nature structural & molecular biology	2007	PMID: 17460694
Identification of the Fanconi anemia complementation group I gene, FANCI.	Dorsman JC	Cellular oncology : the official journal of the International Society for Cellular Oncology	2007	PMID: 17452773

Text-mined citations for this variant ...

Record last updated Mar 05, 2025

ClinVar Genomic variation as it relates to human health

NM_001113378.2(FANCI):c.3116del (p.Tyr1039fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...