5-34911601-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_002853.4(RAD1):c.519G>A(p.Thr173Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,614,126 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_002853.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAD1 | NM_002853.4 | c.519G>A | p.Thr173Thr | synonymous_variant | Exon 4 of 6 | ENST00000382038.7 | NP_002844.1 | |
RAD1 | NR_026591.2 | n.568G>A | non_coding_transcript_exon_variant | Exon 3 of 5 | ||||
TTC23L | NR_169875.1 | n.974-6763C>T | intron_variant | Intron 7 of 15 | ||||
TTC23L | NR_169876.1 | n.1048-6763C>T | intron_variant | Intron 7 of 15 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000749 AC: 114AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000974 AC: 245AN: 251448Hom.: 0 AF XY: 0.00105 AC XY: 143AN XY: 135894
GnomAD4 exome AF: 0.00112 AC: 1631AN: 1461844Hom.: 2 Cov.: 31 AF XY: 0.00110 AC XY: 801AN XY: 727228
GnomAD4 genome AF: 0.000755 AC: 115AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000712 AC XY: 53AN XY: 74458
ClinVar
Submissions by phenotype
RAD1-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at