chr1-15445704-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_007272.3(CTRC):c.747G>T(p.Pro249=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,646 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P249P) has been classified as Likely benign.
Frequency
Consequence
NM_007272.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTRC | NM_007272.3 | c.747G>T | p.Pro249= | synonymous_variant | 7/8 | ENST00000375949.5 | |
CTRC | XM_011540550.2 | c.601G>T | p.Gly201Cys | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTRC | ENST00000375949.5 | c.747G>T | p.Pro249= | synonymous_variant | 7/8 | 1 | NM_007272.3 | P1 | |
CTRC | ENST00000375943.6 | c.*201G>T | 3_prime_UTR_variant | 4/5 | 1 | ||||
CTRC | ENST00000483406.1 | n.511G>T | non_coding_transcript_exon_variant | 5/6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251360Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135882
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461646Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727126
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Hereditary pancreatitis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Dec 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at