rs12432197

chr14-68621468-T-C

Variant summary

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

The ENST00000488612.5(RAD51B):c.1037-29313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,140 control chromosomes in the GnomAD database, including 19,511 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 0.50 (19511 hom., cov: 33)
• Consequence: RAD51B ENST00000488612.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAD51B	NM_001321818.2	c.1037-61469T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51B	ENST00000488612.5	c.1037-29313T>C		intron_variant		1
RAD51B	ENST00000478014.5	n.384-61469T>C		intron_variant, non_coding_transcript_variant		3
RAD51B	ENST00000553595.5	n.614-61469T>C		intron_variant, non_coding_transcript_variant		3
RAD51B	ENST00000554244.5	n.487+57850T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75911 AN: 152020 Hom.: 19483 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.499 AC: 75991 AN: 152140 Hom.: 19511 Cov.: 33 AF XY: 0.498 AC XY: 37013 AN XY: 74370

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.502

Alfa AF: 0.477 Hom.: 24180

Bravo AF: 0.503

Asia WGS AF: 0.412 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	10
Dann	Benign	0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12432197; hg19: chr14-69088185; COSMIC: COSV66854278;