rs7310449

Variant names:

• chr12-912949-G-A
• rs7310449
• NM_134424.4:c.*442C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-912949-G-A
• chr12-912949-G-C
• chr12-912949-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_134424.4(RAD52):​c.*442C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 204,060 control chromosomes in the GnomAD database, including 19,271 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 0.43 (14315 hom., cov: 30)
  • Exomes 𝑓: 0.43 (4956 hom.)
• Consequence: RAD52 NM_134424.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273
• Publications: 15 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 -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 = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD52	NM_134424.4	c.*442C>T		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.*442C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_134424.4	ENSP00000351284.3

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65113 AN: 151576 Hom.: 14297 Cov.: 30

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.411

GnomAD4 exome AF: 0.429 AC: 22470 AN: 52366 Hom.: 4956 Cov.: 0 AF XY: 0.426 AC XY: 10438 AN XY: 24518

African (AFR) AF: 0.346 AC: 818 AN: 2366

American (AMR) AF: 0.512 AC: 753 AN: 1472

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1317 AN: 3306

East Asian (EAS) AF: 0.496 AC: 3911 AN: 7888

South Asian (SAS) AF: 0.303 AC: 149 AN: 492

European-Finnish (FIN) AF: 0.333 AC: 24 AN: 72

Middle Eastern (MID) AF: 0.234 AC: 75 AN: 320

European-Non Finnish (NFE) AF: 0.424 AC: 13598 AN: 32076

Other (OTH) AF: 0.417 AC: 1825 AN: 4374

GnomAD4 genome AF: 0.430 AC: 65163 AN: 151694 Hom.: 14315 Cov.: 30 AF XY: 0.431 AC XY: 31897 AN XY: 74074

African (AFR) AF: 0.362 AC: 14984 AN: 41348

American (AMR) AF: 0.515 AC: 7828 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1404 AN: 3472

East Asian (EAS) AF: 0.531 AC: 2741 AN: 5166

South Asian (SAS) AF: 0.335 AC: 1615 AN: 4816

European-Finnish (FIN) AF: 0.445 AC: 4649 AN: 10452

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

European-Non Finnish (NFE) AF: 0.450 AC: 30539 AN: 67924

Other (OTH) AF: 0.409 AC: 858 AN: 2100

Alfa AF: 0.437 Hom.: 18719

Bravo AF: 0.435

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	1.1
DANN	Benign	0.62
PhyloP100		-0.27
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: rs7310449; hg19: chr12-1022115;