3-4493383-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS1
The NM_001378452.1(ITPR1):c.-315C>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 0.0000388 in 154,502 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001378452.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ITPR1 | NM_001378452.1 | c.-315C>T | 5_prime_UTR_variant | Exon 1 of 62 | ENST00000649015.2 | NP_001365381.1 | ||
ITPR1 | NM_001168272.2 | c.-315C>T | 5_prime_UTR_variant | Exon 1 of 61 | NP_001161744.1 | |||
ITPR1 | NM_001099952.4 | c.-315C>T | 5_prime_UTR_variant | Exon 1 of 59 | NP_001093422.2 | |||
ITPR1 | NM_002222.7 | c.-315C>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.-315C>T | 5_prime_UTR_variant | Exon 1 of 62 | NM_001378452.1 | ENSP00000497605.1 | ||||
ITPR1 | ENST00000354582 | c.-315C>T | 5_prime_UTR_variant | Exon 1 of 62 | 5 | ENSP00000346595.8 | ||||
ITPR1 | ENST00000357086 | c.-315C>T | 5_prime_UTR_variant | Exon 1 of 59 | 1 | ENSP00000349597.4 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152146Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000447 AC: 1AN: 2238Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 1206
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74448
ClinVar
Submissions by phenotype
Autosomal dominant cerebellar ataxia Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at