12-47999661-C-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001844.5(COL2A1):c.292+258G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 17)
Exomes 𝑓: 0.00049 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
COL2A1
NM_001844.5 intron
NM_001844.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.266
Genes affected
COL2A1 (HGNC:2200): (collagen type II alpha 1 chain) This gene encodes the alpha-1 chain of type II collagen, a fibrillar collagen found in cartilage and the vitreous humor of the eye. Mutations in this gene are associated with achondrogenesis, chondrodysplasia, early onset familial osteoarthritis, SED congenita, Langer-Saldino achondrogenesis, Kniest dysplasia, Stickler syndrome type I, and spondyloepimetaphyseal dysplasia Strudwick type. In addition, defects in processing chondrocalcin, a calcium binding protein that is the C-propeptide of this collagen molecule, are also associated with chondrodysplasia. There are two transcripts identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 12-47999661-C-A is Benign according to our data. Variant chr12-47999661-C-A is described in ClinVar as [Benign]. Clinvar id is 670720.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.000494 (19/38448) while in subpopulation EAS AF= 0.00631 (4/634). AF 95% confidence interval is 0.00215. There are 0 homozygotes in gnomad4_exome. There are 10 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAdExome4 at 19 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL2A1 | NM_001844.5 | c.292+258G>T | intron_variant | ENST00000380518.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.292+258G>T | intron_variant | 1 | NM_001844.5 | P1 | |||
COL2A1 | ENST00000337299.7 | c.86-1230G>T | intron_variant | 1 | |||||
COL2A1 | ENST00000474996.6 | n.530+258G>T | intron_variant, non_coding_transcript_variant | 3 | |||||
COL2A1 | ENST00000490609.2 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 115110Hom.: 0 Cov.: 17 FAILED QC
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GnomAD4 exome AF: 0.000494 AC: 19AN: 38448Hom.: 0 Cov.: 0 AF XY: 0.000507 AC XY: 10AN XY: 19706
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GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 115138Hom.: 0 Cov.: 17 AF XY: 0.00 AC XY: 0AN XY: 54734
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at