7-101540037-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001278563.3(COL26A1):c.592A>C(p.Thr198Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,612,486 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign 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. T198M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001278563.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL26A1 | NM_001278563.3 | c.592A>C | p.Thr198Pro | missense_variant | 5/13 | ENST00000313669.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL26A1 | ENST00000313669.12 | c.592A>C | p.Thr198Pro | missense_variant | 5/13 | 1 | NM_001278563.3 | P4 | |
COL26A1 | ENST00000613501.1 | c.586A>C | p.Thr196Pro | missense_variant | 5/13 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000569 AC: 14AN: 245982Hom.: 0 AF XY: 0.0000672 AC XY: 9AN XY: 133924
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460410Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 726544
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | The c.586A>C (p.T196P) alteration is located in exon 5 (coding exon 5) of the COL26A1 gene. This alteration results from a A to C substitution at nucleotide position 586, causing the threonine (T) at amino acid position 196 to be replaced by a proline (P). 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