rs550053089
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 3P and 3B. PM1PP2BP4BP6_Moderate
The NM_000088.4(COL1A1):c.2573C>T(p.Ala858Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,611,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A858G) has been classified as Uncertain significance.
Frequency
Consequence
NM_000088.4 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 | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.2573C>T | p.Ala858Val | missense_variant | 37/51 | ENST00000225964.10 | |
COL1A1 | XM_011524341.2 | c.2375C>T | p.Ala792Val | missense_variant | 34/48 | ||
COL1A1 | XM_005257058.5 | c.2573C>T | p.Ala858Val | missense_variant | 37/49 | ||
COL1A1 | XM_005257059.5 | c.1655C>T | p.Ala552Val | missense_variant | 24/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.2573C>T | p.Ala858Val | missense_variant | 37/51 | 1 | NM_000088.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151780Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000808 AC: 2AN: 247404Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 133992
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459366Hom.: 0 Cov.: 39 AF XY: 0.00000413 AC XY: 3AN XY: 725992
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151900Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74230
ClinVar
Submissions by phenotype
Osteogenesis imperfecta type I Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 05, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at