rs1555571942
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_000088.4(COL1A1):c.3431del(p.Pro1144LeufsTer95) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,457,112 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000088.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL1A1 | NM_000088.4 | c.3431del | p.Pro1144LeufsTer95 | frameshift_variant | 47/51 | ENST00000225964.10 | |
COL1A1 | XM_011524341.2 | c.3233del | p.Pro1078LeufsTer95 | frameshift_variant | 44/48 | ||
COL1A1 | XM_005257058.5 | c.3161del | p.Pro1054LeufsTer95 | frameshift_variant | 45/49 | ||
COL1A1 | XM_005257059.5 | c.2513del | p.Pro838LeufsTer95 | frameshift_variant | 34/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL1A1 | ENST00000225964.10 | c.3431del | p.Pro1144LeufsTer95 | frameshift_variant | 47/51 | 1 | NM_000088.4 | P1 | |
COL1A1 | ENST00000510710.3 | n.8del | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457112Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 724526
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.