5-132640812-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_005732.4(RAD50):c.3752+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,613,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005732.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAD50 | NM_005732.4 | c.3752+7A>G | splice_region_variant, intron_variant | Intron 24 of 24 | ENST00000378823.8 | NP_005723.2 | ||
TH2LCRR | NR_132124.1 | n.45+934T>C | intron_variant | Intron 1 of 2 | ||||
TH2LCRR | NR_132125.1 | n.189+1386T>C | intron_variant | Intron 2 of 2 | ||||
TH2LCRR | NR_132126.1 | n.175-2547T>C | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAD50 | ENST00000378823.8 | c.3752+7A>G | splice_region_variant, intron_variant | Intron 24 of 24 | 1 | NM_005732.4 | ENSP00000368100.4 | |||
ENSG00000283782 | ENST00000640655.2 | c.3455+7A>G | splice_region_variant, intron_variant | Intron 25 of 25 | 5 | ENSP00000491596.2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152030Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251402Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135872
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461846Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727224
GnomAD4 genome AF: 0.000118 AC: 18AN: 152030Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74240
ClinVar
Submissions by phenotype
RAD50-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Hereditary cancer-predisposing syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at