rs11624164

chr14-68519440-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000487861.5(RAD51B):c.1036+51190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,124 control chromosomes in the GnomAD database, including 3,154 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 0.18 (3154 hom., cov: 32)
• Consequence: RAD51B ENST00000487861.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903334	XR_007064223.1	n.17798G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAD51B	ENST00000487270.5	c.1036+51190C>T		intron_variant		1
RAD51B	ENST00000487861.5	c.1036+51190C>T		intron_variant		1
RAD51B	ENST00000488612.5	c.1036+51190C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27380 AN: 152006 Hom.: 3156 Cov.: 32

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.180 AC: 27385 AN: 152124 Hom.: 3154 Cov.: 32 AF XY: 0.180 AC XY: 13353 AN XY: 74384

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.0658

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.163

Alfa AF: 0.231 Hom.: 2220

Bravo AF: 0.168

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	14
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11624164; hg19: chr14-68986157;