chr4-108845250-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_198721.4(COL25A1):āc.1517G>Cā(p.Gly506Ala) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000616 in 1,460,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_198721.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL25A1 | NM_198721.4 | c.1517G>C | p.Gly506Ala | missense_variant, splice_region_variant | 29/38 | ENST00000399132.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL25A1 | ENST00000399132.6 | c.1517G>C | p.Gly506Ala | missense_variant, splice_region_variant | 29/38 | 5 | NM_198721.4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249326Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135262
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460820Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726818
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | The c.1517G>C (p.G506A) alteration is located in exon 29 (coding exon 28) of the COL25A1 gene. This alteration results from a G to C substitution at nucleotide position 1517, causing the glycine (G) at amino acid position 506 to be replaced by an alanine (A). 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