rs1887279

Variant names:

• chr1-183941026-C-A
• rs1887279
• NM_015101.4:c.1398-239G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-183941026-C-A
• chr1-183941026-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015101.4(COLGALT2):​c.1398-239G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COLGALT2	NM_015101.4	c.1398-239G>T		intron_variant	Intron 10 of 11	ENST00000361927.9	NP_055916.1
COLGALT2	NM_001303420.2	c.1398-239G>T		intron_variant	Intron 10 of 11		NP_001290349.1
COLGALT2	NM_001303421.2	c.1038-239G>T		intron_variant	Intron 10 of 11		NP_001290350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COLGALT2	ENST00000361927.9	c.1398-239G>T		intron_variant	Intron 10 of 11	1	NM_015101.4	ENSP00000354960.4
COLGALT2	ENST00000649786.1	c.1398-239G>T		intron_variant	Intron 10 of 11			ENSP00000497601.1
COLGALT2	ENST00000367520.3	c.609-239G>T		intron_variant	Intron 5 of 6	2		ENSP00000356490.3
COLGALT2	ENST00000367521.5	c.222-239G>T		intron_variant	Intron 2 of 3	2		ENSP00000356491.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1433

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.7
DANN	Benign	0.53
PhyloP100		0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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;