NM_138455.4:c.371C>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_138455.4(CTHRC1):c.371C>T(p.Ala124Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000323 in 1,608,254 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138455.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTHRC1 | NM_138455.4 | c.371C>T | p.Ala124Val | missense_variant, splice_region_variant | Exon 2 of 4 | ENST00000330295.10 | NP_612464.1 | |
CTHRC1 | NM_001256099.2 | c.329C>T | p.Ala110Val | missense_variant, splice_region_variant | Exon 2 of 4 | NP_001243028.1 | ||
CTHRC1 | XM_011516824.3 | c.371C>T | p.Ala124Val | missense_variant, splice_region_variant | Exon 2 of 3 | XP_011515126.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTHRC1 | ENST00000330295.10 | c.371C>T | p.Ala124Val | missense_variant, splice_region_variant | Exon 2 of 4 | 1 | NM_138455.4 | ENSP00000330523.5 | ||
CTHRC1 | ENST00000520337.1 | c.329C>T | p.Ala110Val | missense_variant, splice_region_variant | Exon 2 of 4 | 1 | ENSP00000430550.1 | |||
CTHRC1 | ENST00000415886.2 | c.371C>T | p.Ala124Val | missense_variant | Exon 2 of 2 | 2 | ENSP00000416045.2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151872Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000848 AC: 21AN: 247724Hom.: 0 AF XY: 0.0000897 AC XY: 12AN XY: 133838
GnomAD4 exome AF: 0.0000330 AC: 48AN: 1456264Hom.: 0 Cov.: 29 AF XY: 0.0000373 AC XY: 27AN XY: 724456
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151990Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.371C>T (p.A124V) alteration is located in exon 2 (coding exon 2) of the CTHRC1 gene. This alteration results from a C to T substitution at nucleotide position 371, causing the alanine (A) at amino acid position 124 to be replaced by a valine (V). 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