9-114155995-G-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_032888.4(COL27A1):c.45G>A(p.Ala15Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
COL27A1
NM_032888.4 synonymous
NM_032888.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.527
Publications
0 publications found
Genes affected
COL27A1 (HGNC:22986): (collagen type XXVII alpha 1 chain) This gene encodes a member of the fibrillar collagen family, and plays a role during the calcification of cartilage and the transition of cartilage to bone. The encoded protein product is a preproprotein. It includes an N-terminal signal peptide, which is followed by an N-terminal propetide, mature peptide and a C-terminal propeptide. The N-terminal propeptide contains thrombospondin N-terminal-like and laminin G-like domains. The mature peptide is a major triple-helical region. The C-terminal propeptide, also known as COLFI domain, plays crucial roles in tissue growth and repair. Mutations in this gene cause Steel syndrome. Alternatively spliced transcript variants have been found, but the full-length nature of some variants has not been determined. [provided by RefSeq, Sep 2014]
COL27A1 Gene-Disease associations (from GenCC):
- Steel syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 9-114155995-G-A is Benign according to our data. Variant chr9-114155995-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1146332.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.527 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1144808Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 548786
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1144808
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
548786
African (AFR)
AF:
AC:
0
AN:
24682
American (AMR)
AF:
AC:
0
AN:
17258
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
15132
East Asian (EAS)
AF:
AC:
0
AN:
30436
South Asian (SAS)
AF:
AC:
0
AN:
26550
European-Finnish (FIN)
AF:
AC:
0
AN:
28754
Middle Eastern (MID)
AF:
AC:
0
AN:
4556
European-Non Finnish (NFE)
AF:
AC:
0
AN:
951660
Other (OTH)
AF:
AC:
0
AN:
45780
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 07, 2020
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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