12-47973379-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001844.5(COL2A1):c.*28C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000601 in 1,614,144 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001844.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518 | c.*28C>T | 3_prime_UTR_variant | Exon 54 of 54 | 1 | NM_001844.5 | ENSP00000369889.3 | |||
COL2A1 | ENST00000493991.5 | n.3578C>T | non_coding_transcript_exon_variant | Exon 37 of 37 | 2 | |||||
COL2A1 | ENST00000337299.7 | c.*28C>T | downstream_gene_variant | 1 | ENSP00000338213.6 |
Frequencies
GnomAD3 genomes AF: 0.000848 AC: 129AN: 152146Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00150 AC: 377AN: 251496Hom.: 4 AF XY: 0.00144 AC XY: 196AN XY: 135922
GnomAD4 exome AF: 0.000576 AC: 842AN: 1461880Hom.: 5 Cov.: 31 AF XY: 0.000600 AC XY: 436AN XY: 727242
GnomAD4 genome AF: 0.000841 AC: 128AN: 152264Hom.: 1 Cov.: 32 AF XY: 0.00114 AC XY: 85AN XY: 74450
ClinVar
Submissions by phenotype
Stickler syndrome type 1 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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
not provided Benign:1
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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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at