rs11626138

chr14-68320276-A-Gchr14-68320276-A-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+28296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,196 control chromosomes in the GnomAD database, including 21,306 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 0.49 (21306 hom., cov: 33)
• Consequence: RAD51B NM_133510.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAD51B	NM_133510.4	c.853+28296A>G		intron_variant		ENST00000471583.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51B	ENST00000471583.6	c.853+28296A>G		intron_variant		1	NM_133510.4	P4

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74147 AN: 152078 Hom.: 21300 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.487 AC: 74171 AN: 152196 Hom.: 21306 Cov.: 33 AF XY: 0.489 AC XY: 36415 AN XY: 74404

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.470

Alfa AF: 0.549 Hom.: 3094

Bravo AF: 0.464

Asia WGS AF: 0.529 AC: 1841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	16
Dann	Benign	0.47

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: rs11626138; hg19: chr14-68786993;