rs144158633
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005677.4(COLQ):c.394-34C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,567,464 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0069 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00076 ( 17 hom. )
Consequence
COLQ
NM_005677.4 intron
NM_005677.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.568
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 3-15477231-G-A is Benign according to our data. Variant chr3-15477231-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 259858.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00686 (1045/152290) while in subpopulation AFR AF= 0.0236 (981/41554). AF 95% confidence interval is 0.0224. There are 10 homozygotes in gnomad4. There are 492 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLQ | NM_005677.4 | c.394-34C>T | intron_variant | ENST00000383788.10 | |||
COLQ | NM_080538.2 | c.364-34C>T | intron_variant | ||||
COLQ | NM_080539.4 | c.292-34C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLQ | ENST00000383788.10 | c.394-34C>T | intron_variant | 1 | NM_005677.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00676 AC: 1028AN: 152172Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00162 AC: 307AN: 189858Hom.: 3 AF XY: 0.00126 AC XY: 128AN XY: 101290
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GnomAD4 exome AF: 0.000764 AC: 1081AN: 1415174Hom.: 17 Cov.: 26 AF XY: 0.000683 AC XY: 479AN XY: 701296
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GnomAD4 genome ? AF: 0.00686 AC: 1045AN: 152290Hom.: 10 Cov.: 32 AF XY: 0.00661 AC XY: 492AN XY: 74458
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 12, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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