NM_080680.3:c.517C>T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS1_Supporting
The NM_080680.3(COL11A2):c.517C>T(p.Arg173Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,612,982 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00050 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000073 ( 0 hom. )
Consequence
COL11A2
NM_080680.3 missense
NM_080680.3 missense
Scores
1
6
11
Clinical Significance
Conservation
PhyloP100: 2.40
Genes affected
COL11A2 (HGNC:2187): (collagen type XI alpha 2 chain) This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. It is located on chromosome 6 very close to but separate from the gene for retinoid X receptor beta. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Proteolytic processing of this type XI chain produces PARP, a proline/arginine-rich protein that is an amino terminal domain. Mutations in this gene are associated with type III Stickler syndrome, otospondylomegaepiphyseal dysplasia (OSMED syndrome), Weissenbacher-Zweymuller syndrome, autosomal dominant non-syndromic sensorineural type 13 deafness (DFNA13), and autosomal recessive non-syndromic sensorineural type 53 deafness (DFNB53). Alternative splicing results in multiple transcript variants. A related pseudogene is located nearby on chromosome 6. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.022455275).
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000499 (76/152218) while in subpopulation AMR AF= 0.00137 (21/15296). AF 95% confidence interval is 0.000981. There are 0 homozygotes in gnomad4. There are 36 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL11A2 | NM_080680.3 | c.517C>T | p.Arg173Trp | missense_variant | Exon 4 of 66 | ENST00000341947.7 | NP_542411.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL11A2 | ENST00000341947.7 | c.517C>T | p.Arg173Trp | missense_variant | Exon 4 of 66 | 5 | NM_080680.3 | ENSP00000339915.2 | ||
COL11A2 | ENST00000395194.1 | c.517C>T | p.Arg173Trp | missense_variant | Exon 4 of 5 | 1 | ENSP00000378620.1 | |||
COL11A2 | ENST00000374708.8 | c.517C>T | p.Arg173Trp | missense_variant | Exon 4 of 64 | 5 | ENSP00000363840.4 | |||
COL11A2 | ENST00000682718.1 | n.334C>T | non_coding_transcript_exon_variant | Exon 3 of 6 |
Frequencies
GnomAD3 genomes AF: 0.000500 AC: 76AN: 152100Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000158 AC: 39AN: 246566Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134408
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GnomAD4 exome AF: 0.0000726 AC: 106AN: 1460764Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 726692
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GnomAD4 genome AF: 0.000499 AC: 76AN: 152218Hom.: 0 Cov.: 31 AF XY: 0.000484 AC XY: 36AN XY: 74430
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:3Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:2Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 19, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 28, 2024 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34515852) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 10, 2018 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Oct 04, 2015 | The p.Arg173Trp variant in COL11A2 has not been previously reported in individua ls with hearing loss, but has been identified in 0.14% (13/9144) of African chro mosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.or g; dbSNP rs146522169). Although this variant has been seen in the general popula tion, its frequency is not high enough to rule out a pathogenic role. Computatio nal prediction tools and conservation analysis suggest that this variant may imp act the protein, though this information is not predictive enough to determine p athogenicity. In summary, the clinical significance of the p.Arg173Trp variant i s uncertain. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Uncertain
T;T;.;D;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;.;.;.;M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Benign
Sift
Benign
T;D;T;D;D
Sift4G
Uncertain
D;D;D;D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at