rs3010040

Variant names:

• chr1-183939088-C-T
• rs3010040
• NM_015101.4:c.1605-51G>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.1605-51G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 1,430,840 control chromosomes in the GnomAD database, including 27,503 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 0.17 (2298 hom., cov: 32)
  • Exomes 𝑓: 0.19 (25205 hom.)
• Consequence: COLGALT2 NM_015101.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 13 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLGALT2	NM_015101.4	c.1605-51G>A		intron_variant	Intron 11 of 11	ENST00000361927.9	NP_055916.1
COLGALT2	NM_001303420.2	c.1604+1493G>A		intron_variant	Intron 11 of 11		NP_001290349.1
COLGALT2	NM_001303421.2	c.1245-51G>A		intron_variant	Intron 11 of 11		NP_001290350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLGALT2	ENST00000361927.9	c.1605-51G>A		intron_variant	Intron 11 of 11	1	NM_015101.4	ENSP00000354960.4
COLGALT2	ENST00000649786.1	c.1604+1493G>A		intron_variant	Intron 11 of 11			ENSP00000497601.1
COLGALT2	ENST00000367520.3	c.816-51G>A		intron_variant	Intron 6 of 6	2		ENSP00000356490.3
COLGALT2	ENST00000367521.5	c.429-51G>A		intron_variant	Intron 3 of 3	2		ENSP00000356491.1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25124 AN: 151922 Hom.: 2297 Cov.: 32

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.0342

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.188

GnomAD2 exomes AF: 0.204 AC: 45050 AN: 221320 AF XY: 0.203

Gnomad AFR exome AF: 0.0885

Gnomad AMR exome AF: 0.309

Gnomad ASJ exome AF: 0.206

Gnomad EAS exome AF: 0.207

Gnomad FIN exome AF: 0.147

Gnomad NFE exome AF: 0.189

Gnomad OTH exome AF: 0.209

GnomAD4 exome AF: 0.194 AC: 247750 AN: 1278800 Hom.: 25205 Cov.: 17 AF XY: 0.195 AC XY: 124450 AN XY: 638002

African (AFR) AF: 0.0855 AC: 2537 AN: 29666

American (AMR) AF: 0.296 AC: 12279 AN: 41448

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 4686 AN: 23192

East Asian (EAS) AF: 0.247 AC: 9484 AN: 38470

South Asian (SAS) AF: 0.231 AC: 17926 AN: 77600

European-Finnish (FIN) AF: 0.151 AC: 7857 AN: 51914

Middle Eastern (MID) AF: 0.226 AC: 1198 AN: 5308

European-Non Finnish (NFE) AF: 0.190 AC: 181617 AN: 957292

Other (OTH) AF: 0.189 AC: 10166 AN: 53910

GnomAD4 genome AF: 0.165 AC: 25140 AN: 152040 Hom.: 2298 Cov.: 32 AF XY: 0.167 AC XY: 12382 AN XY: 74306

African (AFR) AF: 0.0925 AC: 3836 AN: 41484

American (AMR) AF: 0.253 AC: 3859 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 727 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1067 AN: 5168

South Asian (SAS) AF: 0.227 AC: 1090 AN: 4812

European-Finnish (FIN) AF: 0.144 AC: 1519 AN: 10560

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12553 AN: 67972

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.191 Hom.: 4401

Bravo AF: 0.172

Asia WGS AF: 0.210 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.78
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3010040; hg19: chr1-183908222; COSMIC: COSV62298765;