rs757403373
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001034853.2(RPGR):c.155-10C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,156,118 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 40 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001034853.2 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPGR | NM_001034853.2 | c.155-10C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000645032.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPGR | ENST00000645032.1 | c.155-10C>T | splice_polypyrimidine_tract_variant, intron_variant | NM_001034853.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000358 AC: 4AN: 111711Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33923
GnomAD3 exomes AF: 0.0000327 AC: 6AN: 183319Hom.: 0 AF XY: 0.0000885 AC XY: 6AN XY: 67811
GnomAD4 exome AF: 0.000112 AC: 117AN: 1044407Hom.: 0 Cov.: 24 AF XY: 0.000123 AC XY: 39AN XY: 317503
GnomAD4 genome ? AF: 0.0000358 AC: 4AN: 111711Hom.: 0 Cov.: 23 AF XY: 0.0000295 AC XY: 1AN XY: 33923
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 10, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 26, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at