GeneBe

rs61611291

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_004370.6(COL12A1):​c.9182-105_9182-92delTATATATATATATA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000679 in 147,326 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000068 ( 0 hom. )

Consequence

COL12A1
NM_004370.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.991

Publications

0 publications found
Variant links:
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 2
    Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet
  • Bethlem myopathy 2
    Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Illumina, Genomics England PanelApp
  • Ullrich congenital muscular dystrophy 2
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • Bethlem myopathy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • Ullrich congenital muscular dystrophy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COL12A1NM_004370.6 linkc.9182-105_9182-92delTATATATATATATA intron_variant Intron 65 of 65 ENST00000322507.13 NP_004361.3 Q99715-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COL12A1ENST00000322507.13 linkc.9182-105_9182-92delTATATATATATATA intron_variant Intron 65 of 65 1 NM_004370.6 ENSP00000325146.8 Q99715-1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000679
AC:
1
AN:
147326
Hom.:
0
AF XY:
0.0000122
AC XY:
1
AN XY:
82126
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
2548
American (AMR)
AF:
0.00
AC:
0
AN:
6466
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
4274
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5768
South Asian (SAS)
AF:
0.00
AC:
0
AN:
12824
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
19248
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
544
European-Non Finnish (NFE)
AF:
0.0000112
AC:
1
AN:
89132
Other (OTH)
AF:
0.00
AC:
0
AN:
6522
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.825
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
1017

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.99

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs61611291; hg19: chr6-75796364; API