1-184033740-A-G

Position:

• chr1-184033740-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015101.4(COLGALT2):​c.263+3355T>C 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 151,988 control chromosomes in the GnomAD database, including 3,822 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 (3822 hom., cov: 32)
• Consequence: COLGALT2 NM_015101.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.764

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]

ACMG classification

Verdict is Benign. Variant got -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 = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLGALT2	NM_015101.4	c.263+3355T>C		intron_variant		ENST00000361927.9	NP_055916.1
COLGALT2	NM_001303420.2	c.263+3355T>C		intron_variant			NP_001290349.1
COLGALT2	NM_001303421.2	c.-98+3841T>C		intron_variant			NP_001290350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLGALT2	ENST00000361927.9	c.263+3355T>C		intron_variant		1	NM_015101.4	ENSP00000354960	P1
COLGALT2	ENST00000649786.1	c.263+3355T>C		intron_variant				ENSP00000497601

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33288 AN: 151870 Hom.: 3824 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.219 AC: 33310 AN: 151988 Hom.: 3822 Cov.: 32 AF XY: 0.225 AC XY: 16690 AN XY: 74294

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.217

Alfa AF: 0.207 Hom.: 7439

Bravo AF: 0.220

Asia WGS AF: 0.352 AC: 1224 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	6.1
DANN	Benign	0.82

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

Publications

LitVar

Other links and lift over

dbSNP: rs756199; hg19: chr1-184002874;