chr6-75194844-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_004370.6(COL12A1):c.177G>A(p.Val59Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 1,456,324 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 Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
COL12A1
NM_004370.6 synonymous
NM_004370.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.452
Publications
0 publications found
Genes affected
COL12A1 (HGNC:2188): (collagen type XII alpha 1 chain) This gene encodes the alpha chain of type XII collagen, a member of the FACIT (fibril-associated collagens with interrupted triple helices) collagen family. Type XII collagen is a homotrimer found in association with type I collagen, an association that is thought to modify the interactions between collagen I fibrils and the surrounding matrix. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
COL12A1 Gene-Disease associations (from GenCC):
- Bethlem myopathy 2Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
- Bethlem myopathy 2Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Illumina, Genomics England PanelApp
- Ullrich congenital muscular dystrophy 2Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Bethlem myopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Ullrich congenital muscular dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 6-75194844-C-T is Benign according to our data. Variant chr6-75194844-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 475845.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.452 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL12A1 | ENST00000322507.13 | c.177G>A | p.Val59Val | synonymous_variant | Exon 3 of 66 | 1 | NM_004370.6 | ENSP00000325146.8 | ||
COL12A1 | ENST00000345356.10 | c.73+7876G>A | intron_variant | Intron 2 of 50 | 1 | ENSP00000305147.9 | ||||
COL12A1 | ENST00000483888.6 | c.177G>A | p.Val59Val | synonymous_variant | Exon 3 of 65 | 5 | ENSP00000421216.1 | |||
COL12A1 | ENST00000416123.6 | c.177G>A | p.Val59Val | synonymous_variant | Exon 2 of 63 | 5 | ENSP00000412864.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00000809 AC: 2AN: 247088 AF XY: 0.00000746 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
247088
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1456324Hom.: 0 Cov.: 29 AF XY: 0.00000414 AC XY: 3AN XY: 724554 show subpopulations
GnomAD4 exome
AF:
AC:
7
AN:
1456324
Hom.:
Cov.:
29
AF XY:
AC XY:
3
AN XY:
724554
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33276
American (AMR)
AF:
AC:
0
AN:
44320
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26042
East Asian (EAS)
AF:
AC:
0
AN:
39564
South Asian (SAS)
AF:
AC:
2
AN:
85282
European-Finnish (FIN)
AF:
AC:
0
AN:
53358
Middle Eastern (MID)
AF:
AC:
0
AN:
5756
European-Non Finnish (NFE)
AF:
AC:
5
AN:
1108514
Other (OTH)
AF:
AC:
0
AN:
60212
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.468
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Bethlem myopathy 2;C4225314:Ullrich congenital muscular dystrophy 2 Benign:1
Nov 28, 2023
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
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
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.