1-85737458-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_152890.7(COL24A1):c.4720G>A(p.Glu1574Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,612,986 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL24A1 | ENST00000370571.7 | c.4720G>A | p.Glu1574Lys | missense_variant | Exon 58 of 60 | 1 | NM_152890.7 | ENSP00000359603.2 | ||
COL24A1 | ENST00000426639.5 | n.*2107G>A | non_coding_transcript_exon_variant | Exon 57 of 59 | 5 | ENSP00000409515.1 | ||||
COL24A1 | ENST00000473734.1 | n.130G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 4 | ENSP00000432605.1 | ||||
COL24A1 | ENST00000426639.5 | n.*2107G>A | 3_prime_UTR_variant | Exon 57 of 59 | 5 | ENSP00000409515.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460860Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726748
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4720G>A (p.E1574K) alteration is located in exon 58 (coding exon 58) of the COL24A1 gene. This alteration results from a G to A substitution at nucleotide position 4720, causing the glutamic acid (E) at amino acid position 1574 to be replaced by a lysine (K). 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