chr6-75181216-T-TAA
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_004370.6(COL12A1):c.1892-6_1892-5insTT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000648 in 1,389,228 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 25)
Exomes 𝑓: 0.0000065 ( 0 hom. )
Consequence
COL12A1
NM_004370.6 splice_region, splice_polypyrimidine_tract, intron
NM_004370.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.52
Genes affected
COL12A1 (HGNC:2188): (collagen type XII alpha 1 chain) This gene encodes the alpha chain of type XII collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XII collagen is a homotrimer found in association with type I collagen, an association that is thought to modify the interactions between collagen I fibrils and the surrounding matrix. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.1892-6_1892-5insTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000322507.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.1892-6_1892-5insTT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004370.6 | P4 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 genomes
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25
GnomAD3 exomes AF: 0.00000971 AC: 1AN: 103032Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 55584
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GnomAD4 exome AF: 0.00000648 AC: 9AN: 1389228Hom.: 0 Cov.: 28 AF XY: 0.00000581 AC XY: 4AN XY: 688832
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GnomAD4 genome Cov.: 25
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25
ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at