rs71308146
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_005677.4(COLQ):c.1298+34T>A variant causes a intron 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 Benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
COLQ
NM_005677.4 intron
NM_005677.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.06
Publications
0 publications found
Genes affected
COLQ (HGNC:2226): (collagen like tail subunit of asymmetric acetylcholinesterase) This gene encodes the subunit of a collagen-like molecule associated with acetylcholinesterase in skeletal muscle. Each molecule is composed of three identical subunits. Each subunit contains a proline-rich attachment domain (PRAD) that binds an acetylcholinesterase tetramer to anchor the catalytic subunit of the enzyme to the basal lamina. Mutations in this gene are associated with endplate acetylcholinesterase deficiency. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
COLQ Gene-Disease associations (from GenCC):
- congenital myasthenic syndrome 5Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 3-15453795-A-T is Benign according to our data. Variant chr3-15453795-A-T is described in ClinVar as Benign. ClinVar VariationId is 259852.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005677.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| COLQ | TSL:1 MANE Select | c.1298+34T>A | intron | N/A | ENSP00000373298.3 | Q9Y215-1 | |||
| COLQ | TSL:1 | c.1301+34T>A | intron | N/A | ENSP00000474271.1 | A0A0C4DGS2 | |||
| ENSG00000293553 | TSL:5 | n.*22+34T>A | intron | N/A | ENSP00000518887.1 | A0AAA9YHP9 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1205664Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0AN XY: 608986
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1205664
Hom.:
Cov.:
16
AF XY:
AC XY:
0
AN XY:
608986
African (AFR)
AF:
AC:
0
AN:
28280
American (AMR)
AF:
AC:
0
AN:
40888
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24142
East Asian (EAS)
AF:
AC:
0
AN:
36772
South Asian (SAS)
AF:
AC:
0
AN:
77276
European-Finnish (FIN)
AF:
AC:
0
AN:
51118
Middle Eastern (MID)
AF:
AC:
0
AN:
5276
European-Non Finnish (NFE)
AF:
AC:
0
AN:
890180
Other (OTH)
AF:
AC:
0
AN:
51732
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
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
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