chr12-48000016-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_001844.5(COL2A1):c.195C>T(p.Asp65Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000994 in 1,613,934 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001844.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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COL2A1 | ENST00000380518.8 | c.195C>T | p.Asp65Asp | synonymous_variant | Exon 2 of 54 | 1 | NM_001844.5 | ENSP00000369889.3 | ||
COL2A1 | ENST00000337299.7 | c.86-1585C>T | intron_variant | Intron 1 of 52 | 1 | ENSP00000338213.6 | ||||
COL2A1 | ENST00000474996.6 | n.433C>T | non_coding_transcript_exon_variant | Exon 3 of 8 | 3 | |||||
COL2A1 | ENST00000490609.2 | n.428C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000493 AC: 75AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000349 AC: 87AN: 249534Hom.: 0 AF XY: 0.000303 AC XY: 41AN XY: 135396
GnomAD4 exome AF: 0.00105 AC: 1529AN: 1461624Hom.: 1 Cov.: 32 AF XY: 0.00102 AC XY: 744AN XY: 727128
GnomAD4 genome AF: 0.000492 AC: 75AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74474
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:4
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COL2A1: BP4, BP7 -
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Stickler syndrome type 1 Uncertain:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
not specified Benign:1
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COL2A1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Type II Collagenopathies Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Connective tissue disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at