chr17-50195282-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM5PP2
The NM_000088.4(COL1A1):c.1249C>A(p.Pro417Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,408 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P417A) has been classified as Likely benign.
Frequency
Consequence
NM_000088.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.1249C>A | p.Pro417Thr | missense_variant | 19/51 | ENST00000225964.10 | |
COL1A1 | XM_011524341.2 | c.1051C>A | p.Pro351Thr | missense_variant | 16/48 | ||
COL1A1 | XM_005257058.5 | c.1249C>A | p.Pro417Thr | missense_variant | 19/49 | ||
COL1A1 | XM_005257059.5 | c.957+1032C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.1249C>A | p.Pro417Thr | missense_variant | 19/51 | 1 | NM_000088.4 | P1 | |
COL1A1 | ENST00000471344.1 | n.193C>A | non_coding_transcript_exon_variant | 3/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151838Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461570Hom.: 0 Cov.: 34 AF XY: 0.00000275 AC XY: 2AN XY: 727096
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151838Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74140
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at