NM_000135.4(FANCA):c.4124_4125del (p.Thr1375fs) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Oct 24, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000731876.5

Allele description [Variation Report for NM_000135.4(FANCA):c.4124_4125del (p.Thr1375fs)]

NM_000135.4(FANCA):c.4124_4125del (p.Thr1375fs)

Genes:

FANCA:FA complementation group A [Gene - OMIM - HGNC]
ZNF276:zinc finger protein 276 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_000135.4(FANCA):c.4124_4125del (p.Thr1375fs)

HGVS:

NC_000016.10:g.89739175TG[1]
NG_011706.1:g.82480CA[1]
NM_000135.4:c.4124_4125delMANE SELECT
NM_001113525.2:c.*929TG[1]MANE SELECT
NM_001286167.3:c.4124_4125del
NM_152287.4:c.*929TG[1]
NP_000126.2:p.Thr1375Serfs
NP_000126.2:p.Thr1375fs
NP_001273096.1:p.Thr1375fs
LRG_495t1:c.4122_4123CA[1]
LRG_495:g.82480CA[1]
LRG_495p1:p.Thr1375Serfs
NC_000016.9:g.89805583TG[1]
NC_000016.9:g.89805583_89805584del
NM_000135.2:c.4122_4123CA[1]
NM_000135.2:c.4124_4125del
NM_000135.2:c.4124_4125delCA
NM_000135.2:c.4124_4125delCA
NR_110122.2:n.2929TG[1]
NR_110126.2:n.2812TG[1]
NR_110128.2:n.2752TG[1]
NR_110129.2:n.2846TG[1]

Protein change:

T1375fs

Links:

dbSNP: rs776969626

NCBI 1000 Genomes Browser:

rs776969626

Molecular consequence:

NM_001113525.2:c.*929TG[1] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_152287.4:c.*929TG[1] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000135.4:c.4124_4125del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001286167.3:c.4124_4125del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_110122.2:n.2929TG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110126.2:n.2812TG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110128.2:n.2752TG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110129.2:n.2846TG[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000859739	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Pathogenic (Feb 19, 2018)	germline	clinical testing	Citation Link,
SCV003919630	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Oct 24, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000859739

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)

Pathogenic
(Feb 19, 2018)

germline

clinical testing

Citation Link,

SCV003919630

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Oct 24, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000859739.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

From GeneDx, SCV003919630.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Frameshift variant predicted to result in protein truncation, as the last 81 amino acids are replaced with 48 different amino acids, and other loss-of-function variants have been reported downstream in HGMD; This variant is associated with the following publications: (PMID: 31589614, 24037726, 30792206, 28717661, 27041517, 21273304, 23934222, 26366677)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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