Genetic Variant RAD51:c.-61G>T (chr15-40695367-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_002875.5(RAD51):c.-61G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,416 control chromosomes in the GnomAD database, including 9,734 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 9664 hom., cov: 32)

Exomes 𝑓: 0.39 ( 70 hom. )

Consequence

RAD51
NM_002875.5 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.808

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=-0.87).

BP6

Variant 15-40695367-G-T is Benign according to our data. Variant chr15-40695367-G-T is described in ClinVar as [Benign]. Clinvar id is 1243349.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD51	NM_002875.5 link	c.-61G>T		5_prime_UTR_variant	Exon 1 of 10	ENST00000267868.8	NP_002866.2	Q06609-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
RAD51	ENST00000267868 link	c.-61G>T	5_prime_UTR_variant	Exon 1 of 10	1	NM_002875.5	ENSP00000267868.3	Q06609-1
RAD51	ENST00000557850 link	c.-61G>T	5_prime_UTR_variant	Exon 1 of 8	2		ENSP00000454176.1	Q06609-2
RAD51	ENST00000532743.6 link	c.-262G>T	upstream_gene_variant		2		ENSP00000433924.2	Q06609-1

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52361

AN:

151434

Hom.:

9666

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.369

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.390

Gnomad EAS

AF:

0.0772

Gnomad SAS

AF:

0.234

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.371

GnomAD4 exome

AF:

0.385

AC:

332

AN:

862

Hom.:

Cov.:

AF XY:

0.385

AC XY:

265

AN XY:

688

show subpopulations

Gnomad4 AFR exome

AF:

0.100

Gnomad4 AMR exome

AF:

0.375

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.136

Gnomad4 SAS exome

AF:

0.0909

Gnomad4 FIN exome

AF:

0.286

Gnomad4 NFE exome

AF:

0.408

Gnomad4 OTH exome

AF:

0.208

GnomAD4 genome

AF:

0.345

AC:

52360

AN:

151554

Hom.:

9664

Cov.:

AF XY:

0.337

AC XY:

24977

AN XY:

74104

show subpopulations

Gnomad4 AFR

AF:

0.283

Gnomad4 AMR

AF:

0.313

Gnomad4 ASJ

AF:

0.390

Gnomad4 EAS

AF:

0.0766

Gnomad4 SAS

AF:

0.234

Gnomad4 FIN

AF:

0.306

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.368

Alfa

AF:

0.366

Hom.:

1301

Bravo

AF:

0.340

Asia WGS

AF:

0.150

AC:

523

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 22, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 16398215, 22613844, 17118968) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.8

DANN

Benign

0.62

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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