rs7311151

Variant names:

• chr12-941088-G-A
• rs7311151
• NM_134424.4:c.-18-8012C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-941088-G-A
• chr12-941088-G-C
• chr12-941088-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.-18-8012C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,756 control chromosomes in the GnomAD database, including 25,782 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 0.58 (25782 hom., cov: 32)
• Consequence: RAD52 NM_134424.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 16 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD52	NM_134424.4	c.-18-8012C>T		intron_variant	Intron 1 of 11	ENST00000358495.8	NP_602296.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD52	ENST00000358495.8	c.-18-8012C>T		intron_variant	Intron 1 of 11	1	NM_134424.4	ENSP00000351284.3

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87998 AN: 151634 Hom.: 25757 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.580 AC: 88069 AN: 151756 Hom.: 25782 Cov.: 32 AF XY: 0.581 AC XY: 43106 AN XY: 74136

African (AFR) AF: 0.537 AC: 22199 AN: 41356

American (AMR) AF: 0.682 AC: 10408 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2125 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2696 AN: 5162

South Asian (SAS) AF: 0.642 AC: 3088 AN: 4812

European-Finnish (FIN) AF: 0.535 AC: 5599 AN: 10460

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40078 AN: 67928

Other (OTH) AF: 0.597 AC: 1259 AN: 2110

Alfa AF: 0.592 Hom.: 51628

Bravo AF: 0.587

Asia WGS AF: 0.575 AC: 2000 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		-0.64
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: rs7311151; hg19: chr12-1050254;