chr8-103378120-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_138455.4(CTHRC1):c.466C>T(p.Arg156Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000279 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R156H) has been classified as Uncertain significance.
Frequency
Consequence
NM_138455.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTHRC1 | NM_138455.4 | c.466C>T | p.Arg156Cys | missense_variant | 3/4 | ENST00000330295.10 | |
CTHRC1 | NM_001256099.2 | c.424C>T | p.Arg142Cys | missense_variant | 3/4 | ||
CTHRC1 | XM_011516824.3 | c.372+2161C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTHRC1 | ENST00000330295.10 | c.466C>T | p.Arg156Cys | missense_variant | 3/4 | 1 | NM_138455.4 | P1 | |
CTHRC1 | ENST00000520337.1 | c.424C>T | p.Arg142Cys | missense_variant | 3/4 | 1 | |||
CTHRC1 | ENST00000520880.1 | c.76C>T | p.Arg26Cys | missense_variant | 2/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251226Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135816
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461774Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727196
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.466C>T (p.R156C) alteration is located in exon 3 (coding exon 3) of the CTHRC1 gene. This alteration results from a C to T substitution at nucleotide position 466, causing the arginine (R) at amino acid position 156 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at