chr1-184005004-T-A

Variant names:

• chr1-184005004-T-A
• rs6424922
• NM_015101.4:c.264-26484A>T

Variant summary

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

The NM_015101.4(COLGALT2):​c.264-26484A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,780 control chromosomes in the GnomAD database, including 19,126 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 0.44 (19126 hom., cov: 32)
• Consequence: COLGALT2 NM_015101.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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.264-26484A>T		intron	N/A	NP_055916.1	Q8IYK4
	COLGALT2	NM_001303420.2		c.264-26484A>T		intron	N/A	NP_001290349.1	A0A3B3IT37
	COLGALT2	NM_001303421.2		c.-97-26484A>T		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.264-26484A>T		intron	N/A	ENSP00000354960.4	Q8IYK4
	COLGALT2	ENST00000649786.1		c.264-26484A>T		intron	N/A	ENSP00000497601.1	A0A3B3IT37

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66128 AN: 151662 Hom.: 19065 Cov.: 32

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.437 AC: 66253 AN: 151780 Hom.: 19126 Cov.: 32 AF XY: 0.437 AC XY: 32422 AN XY: 74194

African (AFR) AF: 0.811 AC: 33490 AN: 41300

American (AMR) AF: 0.427 AC: 6521 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 823 AN: 3460

East Asian (EAS) AF: 0.616 AC: 3160 AN: 5134

South Asian (SAS) AF: 0.420 AC: 2024 AN: 4818

European-Finnish (FIN) AF: 0.264 AC: 2792 AN: 10560

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.237 AC: 16130 AN: 67932

Other (OTH) AF: 0.415 AC: 874 AN: 2108

Alfa AF: 0.148 Hom.: 249

Bravo AF: 0.467

Asia WGS AF: 0.547 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
DANN	Benign	0.35
PhyloP100		-1.6
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: rs6424922; hg19: chr1-183974138;