rs12878858

Positions:

• chr14-68320080-G-A
• chr14-68320080-G-C
• chr14-68320080-G-T

Variant summary

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

The NM_133510.4(RAD51B):​c.853+28100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,062 control chromosomes in the GnomAD database, including 22,575 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 0.52 (22575 hom., cov: 32)
• Consequence: RAD51B NM_133510.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802

Genes affected

RAD51B (HGNC:9822): (RAD51 paralog B) The protein encoded by this gene is a member of the RAD51 protein family. RAD51 family members are evolutionarily conserved proteins essential for DNA repair by homologous recombination. This protein has been shown to form a stable heterodimer with the family member RAD51C, which further interacts with the other family members, such as RAD51, XRCC2, and XRCC3. Overexpression of this gene was found to cause cell cycle G1 delay and cell apoptosis, which suggested a role of this protein in sensing DNA damage. Rearrangements between this locus and high mobility group AT-hook 2 (HMGA2, GeneID 8091) have been observed in uterine leiomyomata. [provided by RefSeq, Mar 2016]

RAD51B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAD51B	NM_133510.4	c.853+28100G>A		intron_variant		ENST00000471583.6	NP_598194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAD51B	ENST00000471583.6	c.853+28100G>A		intron_variant		1	NM_133510.4	ENSP00000418859.1

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78985 AN: 151944 Hom.: 22568 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.504

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.520 AC: 79012 AN: 152062 Hom.: 22575 Cov.: 32 AF XY: 0.521 AC XY: 38737 AN XY: 74308

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.505

Alfa AF: 0.568 Hom.: 3175

Bravo AF: 0.501

Asia WGS AF: 0.557 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.27

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: rs12878858; hg19: chr14-68786797;