rs6424922

chr1-184005004-T-Achr1-184005004-T-Cchr1-184005004-T-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COLGALT2	NM_015101.4	c.264-26484A>T		intron_variant		ENST00000361927.9
COLGALT2	NM_001303420.2	c.264-26484A>T		intron_variant
COLGALT2	NM_001303421.2	c.-97-26484A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COLGALT2	ENST00000361927.9	c.264-26484A>T		intron_variant		1	NM_015101.4	P1
COLGALT2	ENST00000649786.1	c.264-26484A>T		intron_variant

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

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.415

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.26
Dann	Benign	0.35

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: rs6424922; hg19: chr1-183974138;