rs369823690
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The ENST00000298854.7(RAPSN):c.790-5T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000384 in 1,606,354 control chromosomes in the GnomAD database, including 1 homozygotes. 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
ENST00000298854.7 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAPSN | NM_005055.5 | c.790-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000298854.7 | NP_005046.2 | |||
LOC124902673 | XR_007062669.1 | n.144+3971A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAPSN | ENST00000298854.7 | c.790-5T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005055.5 | ENSP00000298854 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000722 AC: 11AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000619 AC: 15AN: 242358Hom.: 0 AF XY: 0.0000833 AC XY: 11AN XY: 132122
GnomAD4 exome AF: 0.000417 AC: 606AN: 1454104Hom.: 1 Cov.: 33 AF XY: 0.000441 AC XY: 319AN XY: 723730
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74386
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Fetal akinesia deformation sequence 1;C4225367:Congenital myasthenic syndrome 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at