12-47973422-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001844.5(COL2A1):c.4449G>A(p.Pro1483Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000612 in 1,614,074 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001844.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.4449G>A | p.Pro1483Pro | synonymous_variant | Exon 54 of 54 | 1 | NM_001844.5 | ENSP00000369889.3 | ||
COL2A1 | ENST00000337299.7 | c.4242G>A | p.Pro1414Pro | synonymous_variant | Exon 53 of 53 | 1 | ENSP00000338213.6 | |||
COL2A1 | ENST00000493991.5 | n.3535G>A | non_coding_transcript_exon_variant | Exon 37 of 37 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00327 AC: 498AN: 152062Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000847 AC: 213AN: 251494Hom.: 2 AF XY: 0.000537 AC XY: 73AN XY: 135922
GnomAD4 exome AF: 0.000336 AC: 491AN: 1461894Hom.: 2 Cov.: 31 AF XY: 0.000300 AC XY: 218AN XY: 727248
GnomAD4 genome AF: 0.00327 AC: 497AN: 152180Hom.: 3 Cov.: 32 AF XY: 0.00300 AC XY: 223AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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. -
Connective tissue disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at