chr5-132641435-C-T

Variant names:

• chr5-132641435-C-T
• rs2240032
• NM_005732.4:c.3752+630C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_005732.4(RAD50):​c.3752+630C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,146 control chromosomes in the GnomAD database, including 2,629 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (2629 hom., cov: 32)
• Consequence: RAD50 NM_005732.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.64
• Publications: 33 publications found

Genes affected

RAD50 (HGNC:9816): (RAD50 double strand break repair protein) The protein encoded by this gene is highly similar to Saccharomyces cerevisiae Rad50, a protein involved in DNA double-strand break repair. This protein forms a complex with MRE11 and NBS1. The protein complex binds to DNA and displays numerous enzymatic activities that are required for nonhomologous joining of DNA ends. This protein, cooperating with its partners, is important for DNA double-strand break repair, cell cycle checkpoint activation, telomere maintenance, and meiotic recombination. Knockout studies of the mouse homolog suggest this gene is essential for cell growth and viability. Mutations in this gene are the cause of Nijmegen breakage syndrome-like disorder.[provided by RefSeq, Apr 2010]

ENSG00000283782 (HGNC:):

TH2LCRR (HGNC:40495): (T helper type 2 locus control region associated RNA)

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 5-132641435-C-T is Benign according to our data. Variant chr5-132641435-C-T is described in ClinVar as Benign. ClinVar VariationId is 1248377.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD50	NM_005732.4	c.3752+630C>T		intron_variant	Intron 24 of 24	ENST00000378823.8	NP_005723.2
TH2LCRR	NR_132124.1	n.45+311G>A		intron_variant	Intron 1 of 2
TH2LCRR	NR_132125.1	n.189+763G>A		intron_variant	Intron 2 of 2
TH2LCRR	NR_132126.1	n.175-3170G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD50	ENST00000378823.8	c.3752+630C>T		intron_variant	Intron 24 of 24	1	NM_005732.4	ENSP00000368100.4
ENSG00000283782	ENST00000638452.2	c.3455+630C>T		intron_variant	Intron 26 of 26	5		ENSP00000492349.2

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26832 AN: 152028 Hom.: 2626 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.176 AC: 26837 AN: 152146 Hom.: 2629 Cov.: 32 AF XY: 0.178 AC XY: 13275 AN XY: 74384

African (AFR) AF: 0.0999 AC: 4148 AN: 41528

American (AMR) AF: 0.147 AC: 2254 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 741 AN: 3472

East Asian (EAS) AF: 0.174 AC: 901 AN: 5174

South Asian (SAS) AF: 0.228 AC: 1101 AN: 4826

European-Finnish (FIN) AF: 0.244 AC: 2576 AN: 10576

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.214 AC: 14544 AN: 67958

Other (OTH) AF: 0.184 AC: 390 AN: 2114

Alfa AF: 0.185 Hom.: 1592

Bravo AF: 0.162

Asia WGS AF: 0.188 AC: 655 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 23, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 24661001) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.42
DANN	Benign	0.59
PhyloP100		-1.6
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: rs2240032; hg19: chr5-131977127;