5-178247820-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173465.4(COL23A1):āc.1224A>Gā(p.Ile408Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000454 in 1,612,924 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_173465.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL23A1 | NM_173465.4 | c.1224A>G | p.Ile408Met | missense_variant | 21/29 | ENST00000390654.8 | NP_775736.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL23A1 | ENST00000390654.8 | c.1224A>G | p.Ile408Met | missense_variant | 21/29 | 5 | NM_173465.4 | ENSP00000375069 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000421 AC: 64AN: 152124Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000472 AC: 116AN: 245874Hom.: 0 AF XY: 0.000464 AC XY: 62AN XY: 133550
GnomAD4 exome AF: 0.000458 AC: 669AN: 1460682Hom.: 1 Cov.: 32 AF XY: 0.000472 AC XY: 343AN XY: 726532
GnomAD4 genome AF: 0.000420 AC: 64AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.000457 AC XY: 34AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.1224A>G (p.I408M) alteration is located in exon 21 (coding exon 21) of the COL23A1 gene. This alteration results from a A to G substitution at nucleotide position 1224, causing the isoleucine (I) at amino acid position 408 to be replaced by a methionine (M). 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