NM_015101.4:c.1398-239G>A

Variant names:

• chr1-183941026-C-T
• rs1887279
• NM_015101.4:c.1398-239G>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.1398-239G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,082 control chromosomes in the GnomAD database, including 2,446 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 (2446 hom., cov: 32)
• Consequence: COLGALT2 NM_015101.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.739
• Publications: 8 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015101.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLGALT2	NM_015101.4	MANE Select	c.1398-239G>A		intron	N/A	NP_055916.1	Q8IYK4
	COLGALT2	NM_001303420.2		c.1398-239G>A		intron	N/A	NP_001290349.1	A0A3B3IT37
	COLGALT2	NM_001303421.2		c.1038-239G>A		intron	N/A	NP_001290350.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COLGALT2	ENST00000361927.9	TSL:1 MANE Select	c.1398-239G>A		intron	N/A	ENSP00000354960.4	Q8IYK4
	COLGALT2	ENST00000649786.1		c.1398-239G>A		intron	N/A	ENSP00000497601.1	A0A3B3IT37
	COLGALT2	ENST00000367520.3	TSL:2	c.609-239G>A		intron	N/A	ENSP00000356490.3	Q5SXQ3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26132 AN: 151964 Hom.: 2444 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.172 AC: 26151 AN: 152082 Hom.: 2446 Cov.: 32 AF XY: 0.173 AC XY: 12872 AN XY: 74326

African (AFR) AF: 0.109 AC: 4510 AN: 41480

American (AMR) AF: 0.260 AC: 3966 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3472

East Asian (EAS) AF: 0.207 AC: 1069 AN: 5170

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4820

European-Finnish (FIN) AF: 0.144 AC: 1526 AN: 10564

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12680 AN: 67990

Other (OTH) AF: 0.199 AC: 419 AN: 2110

Alfa AF: 0.175 Hom.: 1433

Bravo AF: 0.179

Asia WGS AF: 0.210 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.55
PhyloP100		0.74
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: rs1887279; hg19: chr1-183910160;