1-85745485-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152890.7(COL24A1):c.4459G>A(p.Ala1487Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,609,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152890.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL24A1 | ENST00000370571.7 | c.4459G>A | p.Ala1487Thr | missense_variant | Exon 56 of 60 | 1 | NM_152890.7 | ENSP00000359603.2 | ||
COL24A1 | ENST00000426639.5 | n.*1846G>A | non_coding_transcript_exon_variant | Exon 55 of 59 | 5 | ENSP00000409515.1 | ||||
COL24A1 | ENST00000426639.5 | n.*1846G>A | 3_prime_UTR_variant | Exon 55 of 59 | 5 | ENSP00000409515.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152100Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000611 AC: 15AN: 245302Hom.: 0 AF XY: 0.0000825 AC XY: 11AN XY: 133318
GnomAD4 exome AF: 0.00000823 AC: 12AN: 1457548Hom.: 0 Cov.: 29 AF XY: 0.0000110 AC XY: 8AN XY: 725132
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152218Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4459G>A (p.A1487T) alteration is located in exon 56 (coding exon 56) of the COL24A1 gene. This alteration results from a G to A substitution at nucleotide position 4459, causing the alanine (A) at amino acid position 1487 to be replaced by a threonine (T). 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