Variant chr15-40698955-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002875.5(RAD51):c.87+110A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0781 in 1,081,130 control chromosomes in the GnomAD database, including 3,733 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.089 ( 629 hom., cov: 32)

Exomes 𝑓: 0.076 ( 3104 hom. )

Consequence

RAD51
NM_002875.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.399

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 15-40698955-A-G is Benign according to our data. Variant chr15-40698955-A-G is described in ClinVar as [Benign]. Clinvar id is 1271457.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAD51	NM_002875.5 linkuse as main transcript	c.87+110A>G		intron_variant		ENST00000267868.8	NP_002866.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAD51	ENST00000267868.8 linkuse as main transcript	c.87+110A>G		intron_variant		1	NM_002875.5	ENSP00000267868	P1	Q06609-1

Frequencies

GnomAD3 genomes

AF:

0.0890

AC:

13541

AN:

152074

Hom.:

625

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.179

Gnomad AMR

AF:

0.0638

Gnomad ASJ

AF:

0.0415

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.0924

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0741

Gnomad OTH

AF:

0.0821

GnomAD4 exome

AF:

0.0763

AC:

70903

AN:

928938

Hom.:

3104

AF XY:

0.0786

AC XY:

37723

AN XY:

480100

show subpopulations

Gnomad4 AFR exome

AF:

0.122

Gnomad4 AMR exome

AF:

0.0687

Gnomad4 ASJ exome

AF:

0.0433

Gnomad4 EAS exome

AF:

0.109

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.0870

Gnomad4 NFE exome

AF:

0.0683

Gnomad4 OTH exome

AF:

0.0804

GnomAD4 genome

AF:

0.0891

AC:

13555

AN:

152192

Hom.:

629

Cov.:

AF XY:

0.0897

AC XY:

6674

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.116

Gnomad4 AMR

AF:

0.0639

Gnomad4 ASJ

AF:

0.0415

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0924

Gnomad4 NFE

AF:

0.0741

Gnomad4 OTH

AF:

0.0822

Alfa

AF:

0.0551

Hom.:

Bravo

AF:

0.0886

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.6

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over