14-68593485-A-G

Position:

• chr14-68593485-A-G

Variant summary

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

The ENST00000487861.5(RAD51B):​c.1037-17521A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,140 control chromosomes in the GnomAD database, including 3,192 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 0.20 (3192 hom., cov: 32)
• Consequence: RAD51B ENST00000487861.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAD51B	NM_001321809.2	c.1037-9178A>G		intron_variant
RAD51B	NM_001321810.2	c.1037-9178A>G		intron_variant
RAD51B	NM_001321815.1	c.923-17673A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51B	ENST00000487270.5	c.1037-1000A>G		intron_variant		1
RAD51B	ENST00000487861.5	c.1037-17521A>G		intron_variant		1
RAD51B	ENST00000488612.5	c.1037-57296A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30291 AN: 152022 Hom.: 3191 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.199 AC: 30313 AN: 152140 Hom.: 3192 Cov.: 32 AF XY: 0.197 AC XY: 14651 AN XY: 74370

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0930

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.188

Alfa AF: 0.211 Hom.: 1744

Bravo AF: 0.198

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4899246; hg19: chr14-69060202;