chr15-40729620-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4BP6_ModerateBP7
The NM_002875.5(RAD51):c.760C>A(p.Arg254Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,802 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
RAD51
NM_002875.5 synonymous
NM_002875.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.23
Publications
5 publications found
Genes affected
RAD51 (HGNC:9817): (RAD51 recombinase) 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, and are known to be involved in the homologous recombination and repair of DNA. This protein can interact with the ssDNA-binding protein RPA and RAD52, and it is thought to play roles in homologous pairing and strand transfer of DNA. This protein is also found to interact with BRCA1 and BRCA2, which may be important for the cellular response to DNA damage. BRCA2 is shown to regulate both the intracellular localization and DNA-binding ability of this protein. Loss of these controls following BRCA2 inactivation may be a key event leading to genomic instability and tumorigenesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]
RAD51 Gene-Disease associations (from GenCC):
- Fanconi anemia complementation group RInheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- mirror movements 2Inheritance: AD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- familial congenital mirror movementsInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Fanconi anemiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- hereditary breast carcinomaInheritance: AD Classification: LIMITED, NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.14).
BP6
Variant 15-40729620-C-A is Benign according to our data. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-40729620-C-A is described in CliVar as Likely_benign. Clinvar id is 3702368.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=3.23 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAD51 | ENST00000267868.8 | c.760C>A | p.Arg254Arg | synonymous_variant | Exon 8 of 10 | 1 | NM_002875.5 | ENSP00000267868.3 | ||
RAD51 | ENST00000532743.6 | c.760C>A | p.Arg254Arg | synonymous_variant | Exon 8 of 10 | 2 | ENSP00000433924.2 | |||
RAD51 | ENST00000557850.5 | c.469C>A | p.Arg157Arg | synonymous_variant | Exon 6 of 8 | 2 | ENSP00000454176.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152114Hom.: 0 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
5
AN:
152114
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251486 AF XY: 0.00000736 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
251486
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461688Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 727138 show subpopulations
GnomAD4 exome
AF:
AC:
20
AN:
1461688
Hom.:
Cov.:
33
AF XY:
AC XY:
14
AN XY:
727138
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33474
American (AMR)
AF:
AC:
0
AN:
44722
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86232
European-Finnish (FIN)
AF:
AC:
0
AN:
53418
Middle Eastern (MID)
AF:
AC:
0
AN:
5636
European-Non Finnish (NFE)
AF:
AC:
17
AN:
1111992
Other (OTH)
AF:
AC:
2
AN:
60378
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.472
Heterozygous variant carriers
0
2
4
5
7
9
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 AF: 0.0000329 AC: 5AN: 152114Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74300 show subpopulations
GnomAD4 genome
AF:
AC:
5
AN:
152114
Hom.:
Cov.:
31
AF XY:
AC XY:
1
AN XY:
74300
show subpopulations
African (AFR)
AF:
AC:
2
AN:
41426
American (AMR)
AF:
AC:
0
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10610
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
3
AN:
68022
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jul 06, 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
Splicing
Name
Calibrated prediction
Score
Prediction
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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