8-103371773-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_138455.4(CTHRC1):c.117G>C(p.Lys39Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,534,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138455.4 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTHRC1 | NM_138455.4 | c.117G>C | p.Lys39Asn | missense_variant | 1/4 | ENST00000330295.10 | |
CTHRC1 | XM_011516824.3 | c.117G>C | p.Lys39Asn | missense_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTHRC1 | ENST00000330295.10 | c.117G>C | p.Lys39Asn | missense_variant | 1/4 | 1 | NM_138455.4 | P1 | |
CTHRC1 | ENST00000415886.2 | c.117G>C | p.Lys39Asn | missense_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000453 AC: 6AN: 132380Hom.: 0 AF XY: 0.0000421 AC XY: 3AN XY: 71292
GnomAD4 exome AF: 0.000192 AC: 266AN: 1382680Hom.: 0 Cov.: 31 AF XY: 0.000173 AC XY: 118AN XY: 681340
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2023 | The c.117G>C (p.K39N) alteration is located in exon 1 (coding exon 1) of the CTHRC1 gene. This alteration results from a G to C substitution at nucleotide position 117, causing the lysine (K) at amino acid position 39 to be replaced by an asparagine (N). 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