Variant 1-183938892-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_015101.4(COLGALT2):c.1750G>A(p.Ala584Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000523 in 1,614,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00031 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00055 ( 0 hom. )

Consequence

COLGALT2
NM_015101.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.587

Variant links:

Genes affected

COLGALT2 (HGNC:16790): (collagen beta(1-O)galactosyltransferase 2) Predicted to enable procollagen galactosyltransferase activity. Predicted to be involved in collagen fibril organization. Predicted to be located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Apr 2022]

COLGALT2 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.03239566).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLGALT2	NM_015101.4 linkuse as main transcript	c.1750G>A	p.Ala584Thr	missense_variant	12/12	ENST00000361927.9	NP_055916.1	Q8IYK4
COLGALT2	NM_001303421.2 linkuse as main transcript	c.1390G>A	p.Ala464Thr	missense_variant	12/12		NP_001290350.1	Q8IYK4B3KT92
COLGALT2	NM_001303420.2 linkuse as main transcript	c.1604+1689G>A		intron_variant			NP_001290349.1	Q8IYK4A0A3B3IT37B4DF84

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
COLGALT2	ENST00000361927.9 linkuse as main transcript	c.1750G>A	p.Ala584Thr	missense_variant	12/12	1	NM_015101.4	ENSP00000354960.4	Q8IYK4
COLGALT2	ENST00000367520.3 linkuse as main transcript	c.961G>A	p.Ala321Thr	missense_variant	7/7	2		ENSP00000356490.3	Q5SXQ3
COLGALT2	ENST00000367521.5 linkuse as main transcript	c.574G>A	p.Ala192Thr	missense_variant	4/4	2		ENSP00000356491.1	Q5SXQ5
COLGALT2	ENST00000649786.1 linkuse as main transcript	c.1604+1689G>A		intron_variant				ENSP00000497601.1	A0A3B3IT37

Frequencies

GnomAD3 genomes

AF:

0.000309

AC:

AN:

152134

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000559

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000402

AC:

101

AN:

251482

Hom.:

AF XY:

0.000419

AC XY:

AN XY:

135916

show subpopulations

Gnomad AFR exome

AF:

0.000123

Gnomad AMR exome

AF:

0.000202

Gnomad ASJ exome

AF:

0.0000992

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.000782

Gnomad OTH exome

AF:

0.000163

GnomAD4 exome

AF:

0.000545

AC:

797

AN:

1461888

Hom.:

Cov.:

AF XY:

0.000549

AC XY:

399

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.0000597

Gnomad4 AMR exome

AF:

0.000201

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000749

Gnomad4 NFE exome

AF:

0.000689

Gnomad4 OTH exome

AF:

0.000248

GnomAD4 genome

AF:

0.000309

AC:

AN:

152134

Hom.:

Cov.:

AF XY:

0.000242

AC XY:

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.000145

Gnomad4 AMR

AF:

0.000131

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000559

Gnomad4 OTH

AF:

0.000478

Alfa

AF:

0.000491

Hom.:

Bravo

AF:

0.000280

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000698

AC:

ExAC

AF:

0.000445

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.000273

EpiControl

AF:

0.000533

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 13, 2022

The c.1750G>A (p.A584T) alteration is located in exon 12 (coding exon 12) of the COLGALT2 gene. This alteration results from a G to A substitution at nucleotide position 1750, causing the alanine (A) at amino acid position 584 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.078

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.47

CADD

Benign

DANN

Uncertain

0.97

DEOGEN2

Benign

0.020

T;T;.

Eigen

Benign

-0.27

Eigen_PC

Benign

-0.069

FATHMM_MKL

Benign

0.74

LIST_S2

Benign

0.63

T;T;T

M_CAP

Benign

0.017

MetaRNN

Benign

0.032

T;T;T

MetaSVM

Benign

-0.76

MutationAssessor

Benign

1.4

.;L;.

PrimateAI

Uncertain

0.63

PROVEAN

Benign

-0.68

N;N;N

REVEL

Benign

0.16

Sift

Benign

0.52

T;T;T

Sift4G

Benign

0.57

T;T;T

Polyphen

0.042, 0.019

.;B;B

Vest4

0.029

MVP

0.72

MPC

0.29

ClinPred

0.030

GERP RS

4.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.097

gMVP

0.42

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