Variant 3-15453794-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005677.4(COLQ):c.1298+35C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0652 in 1,351,064 control chromosomes in the GnomAD database, including 5,089 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1619 hom., cov: 32)

Exomes 𝑓: 0.059 ( 3470 hom. )

Consequence

COLQ
NM_005677.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.310

Variant links:

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 links:

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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=-0.88).

BP6

Variant 3-15453794-G-T is Benign according to our data. Variant chr3-15453794-G-T is described in ClinVar as [Benign]. Clinvar id is 259853.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
COLQ	NM_005677.4 linkuse as main transcript	c.1298+35C>A	intron_variant	ENST00000383788.10
COLQ	NM_080538.2 linkuse as main transcript	c.1268+35C>A	intron_variant
COLQ	NM_080539.4 linkuse as main transcript	c.1196+35C>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COLQ	ENST00000383788.10 linkuse as main transcript	c.1298+35C>A		intron_variant		1	NM_005677.4	P4	Q9Y215-1

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17219

AN:

151884

Hom.:

1606

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.0559

Gnomad EAS

AF:

0.111

Gnomad SAS

AF:

0.0509

Gnomad FIN

AF:

0.0221

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0464

Gnomad OTH

AF:

0.109

GnomAD3 exomes

AF:

0.0871

AC:

18078

AN:

207554

Hom.:

1426

AF XY:

0.0775

AC XY:

8613

AN XY:

111198

show subpopulations

Gnomad AFR exome

AF:

0.247

Gnomad AMR exome

AF:

0.218

Gnomad ASJ exome

AF:

0.0557

Gnomad EAS exome

AF:

0.115

Gnomad SAS exome

AF:

0.0511

Gnomad FIN exome

AF:

0.0255

Gnomad NFE exome

AF:

0.0442

Gnomad OTH exome

AF:

0.0730

GnomAD4 exome

AF:

0.0590

AC:

70773

AN:

1199062

Hom.:

3470

Cov.:

AF XY:

0.0576

AC XY:

34925

AN XY:

605946

show subpopulations

Gnomad4 AFR exome

AF:

0.249

Gnomad4 AMR exome

AF:

0.214

Gnomad4 ASJ exome

AF:

0.0530

Gnomad4 EAS exome

AF:

0.129

Gnomad4 SAS exome

AF:

0.0500

Gnomad4 FIN exome

AF:

0.0279

Gnomad4 NFE exome

AF:

0.0454

Gnomad4 OTH exome

AF:

0.0663

GnomAD4 genome

AF:

0.114

AC:

17270

AN:

152002

Hom.:

1619

Cov.:

AF XY:

0.113

AC XY:

8404

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.242

Gnomad4 AMR

AF:

0.168

Gnomad4 ASJ

AF:

0.0559

Gnomad4 EAS

AF:

0.111

Gnomad4 SAS

AF:

0.0503

Gnomad4 FIN

AF:

0.0221

Gnomad4 NFE

AF:

0.0464

Gnomad4 OTH

AF:

0.109

Alfa

AF:

0.0699

Hom.:

173

Bravo

AF:

0.133

Asia WGS

AF:

0.103

AC:

357

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 16, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.44

DANN

Benign

0.47

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over