1-184013353-C-T

Variant names:

• chr1-184013353-C-T
• rs1952251
• NM_015101.4:c.263+23742G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015101.4(COLGALT2):​c.263+23742G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,982 control chromosomes in the GnomAD database, including 8,607 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (8607 hom., cov: 33)
• Consequence: COLGALT2 NM_015101.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLGALT2	NM_015101.4	c.263+23742G>A		intron_variant	Intron 1 of 11	ENST00000361927.9	NP_055916.1
COLGALT2	NM_001303420.2	c.263+23742G>A		intron_variant	Intron 1 of 11		NP_001290349.1
COLGALT2	NM_001303421.2	c.-98+24228G>A		intron_variant	Intron 1 of 11		NP_001290350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLGALT2	ENST00000361927.9	c.263+23742G>A		intron_variant	Intron 1 of 11	1	NM_015101.4	ENSP00000354960.4
COLGALT2	ENST00000649786.1	c.263+23742G>A		intron_variant	Intron 1 of 11			ENSP00000497601.1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51098 AN: 151864 Hom.: 8587 Cov.: 33

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.322

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.337 AC: 51156 AN: 151982 Hom.: 8607 Cov.: 33 AF XY: 0.337 AC XY: 25021 AN XY: 74296

African (AFR) AF: 0.326 AC: 13519 AN: 41430

American (AMR) AF: 0.319 AC: 4878 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1042 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1720 AN: 5166

South Asian (SAS) AF: 0.377 AC: 1817 AN: 4822

European-Finnish (FIN) AF: 0.316 AC: 3333 AN: 10556

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23732 AN: 67952

Other (OTH) AF: 0.330 AC: 696 AN: 2108

Alfa AF: 0.336 Hom.: 14501

Bravo AF: 0.338

Asia WGS AF: 0.378 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.84
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1952251; hg19: chr1-183982487;