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. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at