rs532650829
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_002906.4(RDX):c.97-10_97-8delTGT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000513 in 1,611,124 control chromosomes in the GnomAD database, including 11 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_002906.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000566 AC: 86AN: 152028Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000857 AC: 215AN: 250794Hom.: 1 AF XY: 0.000981 AC XY: 133AN XY: 135572
GnomAD4 exome AF: 0.000507 AC: 740AN: 1458978Hom.: 11 AF XY: 0.000625 AC XY: 454AN XY: 726002
GnomAD4 genome AF: 0.000572 AC: 87AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.000753 AC XY: 56AN XY: 74400
ClinVar
Submissions by phenotype
not provided Benign:2
See Variant Classification Assertion Criteria. -
- -
not specified Benign:1
c.97-19TGT[3] in intron 3 of RDX: This variant is not expected to have clinical significance because it has been identified in 0.35% (57/16200) of South Asian c hromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute .org). -
RDX-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