rs768531108
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate
The NM_000093.5(COL5A1):c.3086C>A(p.Pro1029Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,456,274 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. P1029L) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.3086C>A | p.Pro1029Gln | missense_variant | 39/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.3086C>A | p.Pro1029Gln | missense_variant | 39/66 | ||
COL5A1 | XM_017014266.3 | c.3086C>A | p.Pro1029Gln | missense_variant | 39/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.3086C>A | p.Pro1029Gln | missense_variant | 39/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.3086C>A | p.Pro1029Gln | missense_variant | 39/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000425 AC: 1AN: 235056Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127470
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456274Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 723774
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centogene AG - the Rare Disease Company | Jun 14, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at