rs41263847
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_001844.5(COL2A1):c.1913C>T(p.Thr638Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000708 in 1,613,620 control chromosomes in the GnomAD database, including 11 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 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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COL2A1 | ENST00000380518.8 | c.1913C>T | p.Thr638Ile | missense_variant | Exon 29 of 54 | 1 | NM_001844.5 | ENSP00000369889.3 | ||
COL2A1 | ENST00000337299.7 | c.1706C>T | p.Thr569Ile | missense_variant | Exon 28 of 53 | 1 | ENSP00000338213.6 | |||
COL2A1 | ENST00000493991.5 | n.837C>T | non_coding_transcript_exon_variant | Exon 12 of 37 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00105 AC: 159AN: 152116Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00242 AC: 604AN: 249176Hom.: 9 AF XY: 0.00226 AC XY: 305AN XY: 135076
GnomAD4 exome AF: 0.000673 AC: 983AN: 1461386Hom.: 10 Cov.: 33 AF XY: 0.000656 AC XY: 477AN XY: 726944
GnomAD4 genome AF: 0.00104 AC: 159AN: 152234Hom.: 1 Cov.: 33 AF XY: 0.00116 AC XY: 86AN XY: 74426
ClinVar
Submissions by phenotype
not specified Benign:4
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not provided Benign:2
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Achondrogenesis type II;C0265279:Kniest dysplasia;C0432214:Namaqualand hip dysplasia;C0432221:Spondylometaphyseal dysplasia - Sutcliffe type;C0700635:Spondyloepimetaphyseal dysplasia, Strudwick type;C0796173:Spondyloperipheral dysplasia;C1442965:Legg-Calve-Perthes disease;C1835437:Platyspondylic dysplasia, Torrance type;C1836080:Stickler syndrome, type I, nonsyndromic ocular;C1836683:Spondyloepiphyseal dysplasia with metatarsal shortening;C1851536:Multiple epiphyseal dysplasia, Beighton type;C1852989:Vitreoretinopathy with phalangeal epiphyseal dysplasia;C2020284:Stickler syndrome type 1;C2745959:Spondyloepiphyseal dysplasia congenita;C4225273:Spondyloepiphyseal dysplasia, Stanescu type;C4551562:Avascular necrosis of femoral head, primary, 1 Benign:1
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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. -
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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Connective tissue disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at