rs11571476

Variant names:

• chr12-912992-T-TA
• rs11571476
• NM_134424.4:c.*398dupT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_134424.4(RAD52):​c.*398dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (14304 hom., cov: 0)
  • Exomes 𝑓: 0.43 (6854 hom.)
• Consequence: RAD52 NM_134424.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD52	NM_134424.4	c.*398dupT		3_prime_UTR_variant	Exon 12 of 12	ENST00000358495.8	NP_602296.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD52	ENST00000358495.8	c.*398dupT		3_prime_UTR_variant	Exon 12 of 12	1	NM_134424.4	ENSP00000351284.3

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65096 AN: 151760 Hom.: 14286 Cov.: 0

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.409

GnomAD4 exome AF: 0.429 AC: 31026 AN: 72280 Hom.: 6854 Cov.: 0 AF XY: 0.424 AC XY: 14369 AN XY: 33862

African (AFR) AF: 0.351 AC: 1153 AN: 3288

American (AMR) AF: 0.513 AC: 1143 AN: 2226

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1718 AN: 4398

East Asian (EAS) AF: 0.494 AC: 4744 AN: 9604

South Asian (SAS) AF: 0.287 AC: 231 AN: 804

European-Finnish (FIN) AF: 0.414 AC: 169 AN: 408

Middle Eastern (MID) AF: 0.264 AC: 117 AN: 444

European-Non Finnish (NFE) AF: 0.426 AC: 19285 AN: 45254

Other (OTH) AF: 0.421 AC: 2466 AN: 5854

GnomAD4 genome AF: 0.429 AC: 65146 AN: 151878 Hom.: 14304 Cov.: 0 AF XY: 0.429 AC XY: 31872 AN XY: 74210

African (AFR) AF: 0.361 AC: 14968 AN: 41406

American (AMR) AF: 0.514 AC: 7844 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1349 AN: 3468

East Asian (EAS) AF: 0.530 AC: 2732 AN: 5158

South Asian (SAS) AF: 0.335 AC: 1618 AN: 4830

European-Finnish (FIN) AF: 0.444 AC: 4666 AN: 10504

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30551 AN: 67952

Other (OTH) AF: 0.407 AC: 856 AN: 2104

Alfa AF: 0.445 Hom.: 1850

Bravo AF: 0.434

Asia WGS AF: 0.409 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11571476; hg19: chr12-1022158; COSMIC: COSV57272111; COSMIC: COSV57272111;