rs2986574

Positions:

• chr1-183937480-G-A
• chr1-183937480-G-C

Variant summary

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

The NM_015101.4(COLGALT2):​c.*1281C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 985,314 control chromosomes in the GnomAD database, including 17,835 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 (2310 hom., cov: 32)
  • Exomes 𝑓: 0.19 (15525 hom.)
• Consequence: COLGALT2 NM_015101.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

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=-0.86).
• 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.*1281C>T		3_prime_UTR_variant	12/12	ENST00000361927.9	NP_055916.1
COLGALT2	NM_001303421.2	c.*1281C>T		3_prime_UTR_variant	12/12		NP_001290350.1
COLGALT2	NM_001303420.2	c.1604+3101C>T		intron_variant			NP_001290349.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLGALT2	ENST00000361927.9	c.*1281C>T		3_prime_UTR_variant	12/12	1	NM_015101.4	ENSP00000354960	P1
COLGALT2	ENST00000367521.5	c.*1281C>T		3_prime_UTR_variant	4/4	2		ENSP00000356491
COLGALT2	ENST00000649786.1	c.1604+3101C>T		intron_variant				ENSP00000497601

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25238 AN: 152014 Hom.: 2309 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.189

GnomAD4 exome AF: 0.192 AC: 159571 AN: 833182 Hom.: 15525 Cov.: 36 AF XY: 0.192 AC XY: 73706 AN XY: 384752

Gnomad4 AFR exome AF: 0.0844

Gnomad4 AMR exome AF: 0.258

Gnomad4 ASJ exome AF: 0.202

Gnomad4 EAS exome AF: 0.198

Gnomad4 SAS exome AF: 0.231

Gnomad4 FIN exome AF: 0.164

Gnomad4 NFE exome AF: 0.193

Gnomad4 OTH exome AF: 0.189

GnomAD4 genome AF: 0.166 AC: 25253 AN: 152132 Hom.: 2310 Cov.: 32 AF XY: 0.167 AC XY: 12425 AN XY: 74378

Gnomad4 AFR AF: 0.0947

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.188

Alfa AF: 0.168 Hom.: 480

Bravo AF: 0.173

Asia WGS AF: 0.210 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.34

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: rs2986574; hg19: chr1-183906614;