rs9332418

Variant names:

• chr1-184032758-C-T
• rs9332418
• NM_015101.4:c.263+4337G>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+4337G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,122 control chromosomes in the GnomAD database, including 3,838 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 0.22 (3838 hom., cov: 33)
• Consequence: COLGALT2 NM_015101.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 9 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLGALT2	NM_015101.4	c.263+4337G>A		intron_variant	Intron 1 of 11	ENST00000361927.9	NP_055916.1
COLGALT2	NM_001303420.2	c.263+4337G>A		intron_variant	Intron 1 of 11		NP_001290349.1
COLGALT2	NM_001303421.2	c.-98+4823G>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+4337G>A		intron_variant	Intron 1 of 11	1	NM_015101.4	ENSP00000354960.4
COLGALT2	ENST00000649786.1	c.263+4337G>A		intron_variant	Intron 1 of 11			ENSP00000497601.1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33339 AN: 152004 Hom.: 3840 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.219 AC: 33361 AN: 152122 Hom.: 3838 Cov.: 33 AF XY: 0.225 AC XY: 16716 AN XY: 74356

African (AFR) AF: 0.195 AC: 8095 AN: 41502

American (AMR) AF: 0.236 AC: 3610 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2423 AN: 5172

South Asian (SAS) AF: 0.280 AC: 1353 AN: 4824

European-Finnish (FIN) AF: 0.239 AC: 2529 AN: 10570

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14046 AN: 67986

Other (OTH) AF: 0.218 AC: 461 AN: 2112

Alfa AF: 0.201 Hom.: 412

Bravo AF: 0.220

Asia WGS AF: 0.351 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.5
DANN	Benign	0.51
PhyloP100		-0.16
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: rs9332418; hg19: chr1-184001892;