rs4902623

chr14-68644209-G-Achr14-68644209-G-Cchr14-68644209-G-T

Variant summary

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

The ENST00000488612.5(RAD51B):c.1037-6572G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,108 control chromosomes in the GnomAD database, including 29,364 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 0.62 (29364 hom., cov: 32)
• Consequence: RAD51B ENST00000488612.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146

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]

LOC124903333 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903333	XR_007064220.1	n.300-6132C>T		intron_variant, non_coding_transcript_variant
RAD51B	NM_001321818.2	c.1037-38728G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51B	ENST00000488612.5	c.1037-6572G>A		intron_variant		1
RAD51B	ENST00000478014.5	n.384-38728G>A		intron_variant, non_coding_transcript_variant		3
RAD51B	ENST00000553595.5	n.614-38728G>A		intron_variant, non_coding_transcript_variant		3
RAD51B	ENST00000554244.5	n.488-38728G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93617 AN: 151990 Hom.: 29332 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.616 AC: 93698 AN: 152108 Hom.: 29364 Cov.: 32 AF XY: 0.623 AC XY: 46334 AN XY: 74386

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.622

Alfa AF: 0.584 Hom.: 14828

Bravo AF: 0.622

Asia WGS AF: 0.828 AC: 2879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.0
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4902623; hg19: chr14-69110926;