12-47978015-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PP2PP3_ModerateBP6BS2
The NM_001844.5(COL2A1):āc.3106C>Gā(p.Arg1036Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,156 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001844.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.3106C>G | p.Arg1036Gly | missense_variant | Exon 44 of 54 | 1 | NM_001844.5 | ENSP00000369889.3 | ||
COL2A1 | ENST00000337299.7 | c.2899C>G | p.Arg967Gly | missense_variant | Exon 43 of 53 | 1 | ENSP00000338213.6 | |||
COL2A1 | ENST00000493991.5 | n.2192C>G | non_coding_transcript_exon_variant | Exon 27 of 37 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 249916Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135382
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461076Hom.: 3 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 726848
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
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In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 30753492) -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at