12-915428-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000358495.8(RAD52):​c.866-896C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,090 control chromosomes in the GnomAD database, including 14,035 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 0.42 ( 14035 hom., cov: 32)

Consequence

RAD52
ENST00000358495.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04
Variant links:
Genes affected
RAD52 (HGNC:9824): (RAD52 homolog, DNA repair protein) The protein encoded by this gene shares similarity with Saccharomyces cerevisiae Rad52, a protein important for DNA double-strand break repair and homologous recombination. This gene product was shown to bind single-stranded DNA ends, and mediate the DNA-DNA interaction necessary for the annealing of complementary DNA strands. It was also found to interact with DNA recombination protein RAD51, which suggested its role in RAD51 related DNA recombination and repair. A pseudogene of this gene is present on chromosome 2. Alternative splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Jul 2014]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RAD52NM_134424.4 linkuse as main transcriptc.866-896C>A intron_variant ENST00000358495.8 NP_602296.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RAD52ENST00000358495.8 linkuse as main transcriptc.866-896C>A intron_variant 1 NM_134424.4 ENSP00000351284 P2P43351-1

Frequencies

GnomAD3 genomes
AF:
0.424
AC:
64482
AN:
151972
Hom.:
14017
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.348
Gnomad AMI
AF:
0.531
Gnomad AMR
AF:
0.511
Gnomad ASJ
AF:
0.403
Gnomad EAS
AF:
0.528
Gnomad SAS
AF:
0.336
Gnomad FIN
AF:
0.441
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.448
Gnomad OTH
AF:
0.410
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.424
AC:
64530
AN:
152090
Hom.:
14035
Cov.:
32
AF XY:
0.426
AC XY:
31636
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.348
Gnomad4 AMR
AF:
0.512
Gnomad4 ASJ
AF:
0.403
Gnomad4 EAS
AF:
0.528
Gnomad4 SAS
AF:
0.335
Gnomad4 FIN
AF:
0.441
Gnomad4 NFE
AF:
0.448
Gnomad4 OTH
AF:
0.408
Alfa
AF:
0.436
Hom.:
29481
Bravo
AF:
0.429
Asia WGS
AF:
0.408
AC:
1417
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.50
DANN
Benign
0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10744729; hg19: chr12-1024594; API