rs12588940

Positions:

• chr14-68565151-T-A
• chr14-68565151-T-C
• chr14-68565151-T-G

Variant summary

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

The ENST00000487861.5(RAD51B):​c.1037-45855T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,052 control chromosomes in the GnomAD database, including 5,034 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 0.25 (5034 hom., cov: 33)
• Consequence: RAD51B ENST00000487861.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

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]

LOC124903335 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903335	XR_007064225.1	n.100A>T		splice_region_variant, non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAD51B	ENST00000487270.5	c.1037-29334T>A		intron_variant		1		ENSP00000419471
RAD51B	ENST00000487861.5	c.1037-45855T>A		intron_variant		1		ENSP00000419881
RAD51B	ENST00000488612.5	c.1037-85630T>A		intron_variant		1		ENSP00000420061

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38674 AN: 151934 Hom.: 5012 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.255 AC: 38735 AN: 152052 Hom.: 5034 Cov.: 33 AF XY: 0.254 AC XY: 18861 AN XY: 74318

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.269

Alfa AF: 0.257 Hom.: 643

Bravo AF: 0.259

Asia WGS AF: 0.336 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.074
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12588940; hg19: chr14-69031868;