rs4902610

Positions:

• chr14-68607109-C-T

Variant summary

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

The ENST00000487861.5(RAD51B):​c.1037-3897C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,092 control chromosomes in the GnomAD database, including 5,052 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 0.24 (5052 hom., cov: 32)
• Consequence: RAD51B ENST00000487861.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984016	XR_943973.3	n.746-623G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661958.1	n.1926-623G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37184 AN: 151974 Hom.: 5036 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.245 AC: 37241 AN: 152092 Hom.: 5052 Cov.: 32 AF XY: 0.251 AC XY: 18695 AN XY: 74370

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.237

Alfa AF: 0.227 Hom.: 4753

Bravo AF: 0.252

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4902610; hg19: chr14-69073826;