17-35107131-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_002878.4(RAD51D):c.346-9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,624 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
RAD51D
NM_002878.4 intron
NM_002878.4 intron
Scores
2
Splicing: ADA: 0.0001469
2
Clinical Significance
Conservation
PhyloP100: 0.0870
Publications
0 publications found
Genes affected
RAD51D (HGNC:9823): (RAD51 paralog D) The protein encoded by this gene is a member of the RAD51 protein family. RAD51 family members are highly similar to bacterial RecA and Saccharomyces cerevisiae Rad51, which are known to be involved in the homologous recombination and repair of DNA. This protein forms a complex with several other members of the RAD51 family, including RAD51L1, RAD51L2, and XRCC2. The protein complex formed with this protein has been shown to catalyze homologous pairing between single- and double-stranded DNA, and is thought to play a role in the early stage of recombinational repair of DNA. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream ring finger and FYVE-like domain containing 1 (RFFL) gene. [provided by RefSeq, Jan 2011]
RAD51D Gene-Disease associations (from GenCC):
- breast-ovarian cancer, familial, susceptibility to, 4Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
- hereditary breast ovarian cancer syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- hereditary breast carcinomaInheritance: AD Classification: LIMITED Submitted by: ClinGen
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
Variant 17-35107131-G-T is Benign according to our data. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397. Variant chr17-35107131-G-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 239397.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461624Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727112 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461624
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
727112
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33478
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86242
European-Finnish (FIN)
AF:
AC:
0
AN:
53266
Middle Eastern (MID)
AF:
AC:
0
AN:
5686
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1112000
Other (OTH)
AF:
AC:
0
AN:
60392
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1
Feb 14, 2024
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
The RAD51D c.346-9C>A variant has not been reported in individuals with RAD51D-related conditions in the published literature. It also has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on RAD51D mRNA splicing yielded inconclusive findings. Based on the available information, we are unable to determine the clinical significance of this variant. -
Hereditary cancer-predisposing syndrome Benign:1
Feb 29, 2016
Color Diagnostics, LLC DBA Color Health
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Breast-ovarian cancer, familial, susceptibility to, 4 Benign:1
Jul 24, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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