NM_002878.4(RAD51D):c.904-3C>T AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (3 submissions)
Last evaluated:: Jul 2, 2021
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:: RCV000130350.21

Allele description [Variation Report for NM_002878.4(RAD51D):c.904-3C>T]

NM_002878.4(RAD51D):c.904-3C>T

Genes:

RAD51D:RAD51 paralog D [Gene - OMIM - HGNC]
RAD51L3-RFFL:RAD51L3-RFFL readthrough [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

17q12

Genomic location:

Preferred name:

NM_002878.4(RAD51D):c.904-3C>T

HGVS:

NC_000017.11:g.35101039G>A
NG_031858.1:g.23831C>T
NM_001142571.2:c.964-3C>T
NM_002878.4:c.904-3C>TMANE SELECT
NM_133629.3:c.568-3C>T
LRG_516t1:c.904-3C>T
LRG_516:g.23831C>T
NC_000017.10:g.33428058G>A
NM_002878.3:c.904-3C>T

Links:

dbSNP: rs45478491

NCBI 1000 Genomes Browser:

rs45478491

Molecular consequence:

NM_001142571.2:c.964-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_002878.4:c.904-3C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_133629.3:c.568-3C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000185201	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Sep 19, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21822267, 22415235 Citation Link,
SCV000691378	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 11, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002527050	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Likely benign (Jul 2, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000185201

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Sep 19, 2018)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV000691378

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Apr 11, 2016)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002527050

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Likely benign
(Jul 2, 2021)

germline

curation

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Germline mutations in RAD51D confer susceptibility to ovarian cancer.

Loveday C, Turnbull C, Ramsay E, Hughes D, Ruark E, Frankum JR, Bowden G, Kalmyrzaev B, Warren-Perry M, Snape K, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Brice G, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Greenhalgh L, et al.

Nat Genet. 2011 Aug 7;43(9):879-882. doi: 10.1038/ng.893.

PubMed [citation]

PMID:: 21822267
PMCID:: PMC4845885

Mutation analysis of RAD51D in non-BRCA1/2 ovarian and breast cancer families.

Osher DJ, De Leeneer K, Michils G, Hamel N, Tomiak E, Poppe B, Leunen K, Legius E, Shuen A, Smith E, Arseneau J, Tonin P, Matthijs G, Claes K, Tischkowitz MD, Foulkes WD.

Br J Cancer. 2012 Apr 10;106(8):1460-3. doi: 10.1038/bjc.2012.87. Epub 2012 Mar 13.

PubMed [citation]

PMID:: 22415235
PMCID:: PMC3326673

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV000185201.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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		not provided	not provided	not provided	not provided

From Color Diagnostics, LLC DBA Color Health, SCV000691378.2

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

#	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		not provided	not provided	not provided	not provided

From Sema4, Sema4, SCV002527050.1

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

Last Updated: Nov 24, 2024

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