rs558804336
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001378452.1(ITPR1):c.2780-8T>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 0.0000062 in 1,612,782 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 Uncertain significance (★).
Frequency
Consequence
NM_001378452.1 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.2780-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000649015.2 | |||
ITPR1 | NM_001099952.4 | c.2753-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ITPR1 | NM_001168272.2 | c.2735-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
ITPR1 | NM_002222.7 | c.2708-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015.2 | c.2780-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_001378452.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152138Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247324Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134128
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460526Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726506
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152256Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 26, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at