rs41317925
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The ENST00000380518.8(COL2A1):c.1545C>T(p.Arg515=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,551,642 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R515R) has been classified as Likely benign.
Frequency
Consequence
ENST00000380518.8 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL2A1 | NM_001844.5 | c.1545C>T | p.Arg515= | synonymous_variant | 24/54 | ENST00000380518.8 | NP_001835.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.1545C>T | p.Arg515= | synonymous_variant | 24/54 | 1 | NM_001844.5 | ENSP00000369889 | P1 | |
COL2A1 | ENST00000337299.7 | c.1338C>T | p.Arg446= | synonymous_variant | 23/53 | 1 | ENSP00000338213 | |||
COL2A1 | ENST00000493991.5 | n.469C>T | non_coding_transcript_exon_variant | 7/37 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 5AN: 156540Hom.: 0 AF XY: 0.0000486 AC XY: 4AN XY: 82352
GnomAD4 exome AF: 0.0000186 AC: 26AN: 1399402Hom.: 0 Cov.: 34 AF XY: 0.0000232 AC XY: 16AN XY: 690218
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 16, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at