rs752652515
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_004370.6(COL12A1):c.1892-6_1892-5insT 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 0.0000668 in 1,406,404 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00043 ( 0 hom., cov: 25)
Exomes 𝑓: 0.000062 ( 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
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 Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant 6-75181216-T-TA is Benign according to our data. Variant chr6-75181216-T-TA is described in ClinVar as [Benign]. Clinvar id is 1165668.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL12A1 | NM_004370.6 | c.1892-6_1892-5insT | 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_1892-5insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004370.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000430 AC: 8AN: 18588Hom.: 0 Cov.: 25
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GnomAD3 exomes AF: 0.000194 AC: 20AN: 103032Hom.: 0 AF XY: 0.000180 AC XY: 10AN XY: 55584
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GnomAD4 exome AF: 0.0000620 AC: 86AN: 1387792Hom.: 0 Cov.: 28 AF XY: 0.0000770 AC XY: 53AN XY: 688080
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GnomAD4 genome ? AF: 0.000430 AC: 8AN: 18612Hom.: 0 Cov.: 25 AF XY: 0.000439 AC XY: 4AN XY: 9102
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 08, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at