rs3010040

Positions:

• chr1-183939088-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• 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/exons	MANE	Protein	UniProt
COLGALT2	NM_015101.4	c.1605-51G>A		intron_variant		ENST00000361927.9	NP_055916.1
COLGALT2	NM_001303420.2	c.1604+1493G>A		intron_variant			NP_001290349.1
COLGALT2	NM_001303421.2	c.1245-51G>A		intron_variant			NP_001290350.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLGALT2	ENST00000361927.9	c.1605-51G>A		intron_variant		1	NM_015101.4	ENSP00000354960.4
COLGALT2	ENST00000649786.1	c.1604+1493G>A		intron_variant				ENSP00000497601.1
COLGALT2	ENST00000367520.3	c.816-51G>A		intron_variant		2		ENSP00000356490.3
COLGALT2	ENST00000367521.5	c.429-51G>A		intron_variant		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

GnomAD3 exomes AF: 0.204 AC: 45050 AN: 221320 Hom.: 4892 AF XY: 0.203 AC XY: 24137 AN XY: 118732

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 SAS exome AF: 0.236

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

Gnomad4 AFR exome AF: 0.0855

Gnomad4 AMR exome AF: 0.296

Gnomad4 ASJ exome AF: 0.202

Gnomad4 EAS exome AF: 0.247

Gnomad4 SAS exome AF: 0.231

Gnomad4 FIN exome AF: 0.151

Gnomad4 NFE exome AF: 0.190

Gnomad4 OTH exome AF: 0.189

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

Gnomad4 AFR AF: 0.0925

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.187

Alfa AF: 0.195 Hom.: 3183

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs3010040; hg19: chr1-183908222; COSMIC: COSV62298765;