rs886038490
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001844.5(COL2A1):c.2376C>T(p.Gly792=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G792G) has been classified as Likely benign.
Frequency
Consequence
NM_001844.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL2A1 | NM_001844.5 | c.2376C>T | p.Gly792= | synonymous_variant | 36/54 | ENST00000380518.8 | |
LOC105369752 | XR_944910.2 | n.218+383G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.2376C>T | p.Gly792= | synonymous_variant | 36/54 | 1 | NM_001844.5 | P1 | |
COL2A1 | ENST00000337299.7 | c.2169C>T | p.Gly723= | synonymous_variant | 35/53 | 1 | |||
COL2A1 | ENST00000483376.1 | n.554C>T | non_coding_transcript_exon_variant | 7/8 | 5 | ||||
COL2A1 | ENST00000493991.5 | n.1462C>T | non_coding_transcript_exon_variant | 19/37 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1402300Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 692070
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.