rs7180135

Positions:

• chr15-40731896-G-A
• chr15-40731896-G-C
• chr15-40731896-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002875.5(RAD51):​c.*718G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 211,414 control chromosomes in the GnomAD database, including 44,986 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.64 (32142 hom., cov: 31)
  • Exomes 𝑓: 0.64 (12844 hom.)
• Consequence: RAD51 NM_002875.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAD51	NM_002875.5	c.*718G>A		3_prime_UTR_variant	10/10	ENST00000267868.8	NP_002866.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAD51	ENST00000267868.8	c.*718G>A		3_prime_UTR_variant	10/10	1	NM_002875.5	ENSP00000267868.3
RAD51	ENST00000645673.2	c.*718G>A		3_prime_UTR_variant	10/10			ENSP00000493712.2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97758 AN: 151882 Hom.: 32086 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.616

GnomAD4 exome AF: 0.642 AC: 38163 AN: 59414 Hom.: 12844 Cov.: 0 AF XY: 0.641 AC XY: 17677 AN XY: 27588

Gnomad4 AFR exome AF: 0.698

Gnomad4 AMR exome AF: 0.705

Gnomad4 ASJ exome AF: 0.603

Gnomad4 EAS exome AF: 0.959

Gnomad4 SAS exome AF: 0.760

Gnomad4 FIN exome AF: 0.556

Gnomad4 NFE exome AF: 0.564

Gnomad4 OTH exome AF: 0.628

GnomAD4 genome AF: 0.644 AC: 97877 AN: 152000 Hom.: 32142 Cov.: 31 AF XY: 0.654 AC XY: 48557 AN XY: 74286

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.619

Alfa AF: 0.622 Hom.: 3675

Bravo AF: 0.648

Asia WGS AF: 0.845 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.24

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

Other links and lift over

dbSNP: rs7180135; hg19: chr15-41024094;