1-15438464-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007272.3(CTRC):c.-1C>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 0.0000155 in 1,614,044 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 Uncertain significance (★).
Frequency
Consequence
NM_007272.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTRC | ENST00000375949 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 8 | 1 | NM_007272.3 | ENSP00000365116.4 | |||
CTRC | ENST00000375943 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 5 | 1 | ENSP00000365110.2 | ||||
CTRC | ENST00000476813.5 | n.12C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251466Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135906
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461864Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727228
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74336
ClinVar
Submissions by phenotype
Hereditary pancreatitis Uncertain:1
The c.-1C>T variant is located in the 5' untranslated region (5’ UTR) of the CTRC gene. This variant results from a C to T substitution 1 bases upstream from the first translated codon. This alteration was detected in one individual with chronic pancreatitis; however, clinical details were limited (Zhou J et al. J Gastroenterol Hepatol, 2011 Aug;26:1238-46). Based on nucleotide sequence alignment, this nucleotide position is well conserved in available vertebrate species. Based on the available evidence, the clinical significance of this variant remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at