chr14-68536271-A-G

Position:

• chr14-68536271-A-G

Variant summary

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

The ENST00000487861.5(RAD51B):​c.1036+68021A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,050 control chromosomes in the GnomAD database, including 19,091 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 0.49 (19091 hom., cov: 32)
• Consequence: RAD51B ENST00000487861.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719

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]

LOC124903334 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903334	XR_007064223.1	n.1234T>C		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51B	ENST00000487270.5	c.1037-58214A>G		intron_variant		1
RAD51B	ENST00000487861.5	c.1036+68021A>G		intron_variant		1
RAD51B	ENST00000488612.5	c.1036+68021A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74462 AN: 151932 Hom.: 19078 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.490 AC: 74499 AN: 152050 Hom.: 19091 Cov.: 32 AF XY: 0.489 AC XY: 36332 AN XY: 74318

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.493

Alfa AF: 0.552 Hom.: 41078

Bravo AF: 0.490

Asia WGS AF: 0.559 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2189517; hg19: chr14-69002988;