3-4493555-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001378452.1(ITPR1):c.-143C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001378452.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 62 | ENST00000649015.2 | NP_001365381.1 | ||
ITPR1 | NM_001168272.2 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 61 | NP_001161744.1 | |||
ITPR1 | NM_001099952.4 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 59 | NP_001093422.2 | |||
ITPR1 | NM_002222.7 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 58 | NP_002213.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ITPR1 | ENST00000649015 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 62 | NM_001378452.1 | ENSP00000497605.1 | ||||
ITPR1 | ENST00000354582 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 62 | 5 | ENSP00000346595.8 | ||||
ITPR1 | ENST00000648266 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 62 | ENSP00000498014.1 | |||||
ITPR1 | ENST00000443694 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 61 | 1 | ENSP00000401671.2 | ||||
ITPR1 | ENST00000357086 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 59 | 1 | ENSP00000349597.4 | ||||
ITPR1 | ENST00000456211 | c.-143C>T | 5_prime_UTR_variant | Exon 1 of 58 | 1 | ENSP00000397885.2 | ||||
ITPR1 | ENST00000650294.1 | c.-143C>T | upstream_gene_variant | ENSP00000498056.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 784Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 480
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at