Variant chr19-17555827-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_024656.4(COLGALT1):c.114C>T(p.Phe38Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 1,298,894 control chromosomes in the GnomAD database, including 192,087 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.44 ( 16699 hom., cov: 33)

Exomes 𝑓: 0.55 ( 175388 hom. )

Consequence

COLGALT1
NM_024656.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.618

Variant links:

Genes affected

COLGALT1 (HGNC:26182): (collagen beta(1-O)galactosyltransferase 1) The protein encoded by this gene is one of two enzymes that transfers galactose moieties to hydroxylysine residues of collagen and mannose binding lectin. This gene is constitutively expressed and encodes a soluble protein that localizes to the endoplasmic reticulum. [provided by RefSeq, Dec 2015]

COLGALT1 links:

COLGALT1 (HGNC:):

COLGALT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 19-17555827-C-T is Benign according to our data. Variant chr19-17555827-C-T is described in ClinVar as [Benign]. Clinvar id is 1924834.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.618 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COLGALT1	NM_024656.4 linkuse as main transcript	c.114C>T	p.Phe38Phe	synonymous_variant	1/12	ENST00000252599.9	NP_078932.2	Q8NBJ5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COLGALT1	ENST00000252599.9 linkuse as main transcript	c.114C>T	p.Phe38Phe	synonymous_variant	1/12	1	NM_024656.4	ENSP00000252599.3		Q8NBJ5

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66555

AN:

151328

Hom.:

16700

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.448

Gnomad AMR

AF:

0.425

Gnomad ASJ

AF:

0.633

Gnomad EAS

AF:

0.352

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.561

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.563

Gnomad OTH

AF:

0.492

GnomAD3 exomes

AF:

0.491

AC:

10728

AN:

21858

Hom.:

2802

AF XY:

0.493

AC XY:

6837

AN XY:

13872

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.329

Gnomad ASJ exome

AF:

0.603

Gnomad EAS exome

AF:

0.354

Gnomad SAS exome

AF:

0.431

Gnomad FIN exome

AF:

0.561

Gnomad NFE exome

AF:

0.553

Gnomad OTH exome

AF:

0.515

GnomAD4 exome

AF:

0.547

AC:

627095

AN:

1147458

Hom.:

175388

Cov.:

AF XY:

0.546

AC XY:

302608

AN XY:

554214

show subpopulations

Gnomad4 AFR exome

AF:

0.182

Gnomad4 AMR exome

AF:

0.365

Gnomad4 ASJ exome

AF:

0.612

Gnomad4 EAS exome

AF:

0.301

Gnomad4 SAS exome

AF:

0.442

Gnomad4 FIN exome

AF:

0.552

Gnomad4 NFE exome

AF:

0.569

Gnomad4 OTH exome

AF:

0.523

GnomAD4 genome

AF:

0.440

AC:

66562

AN:

151436

Hom.:

16699

Cov.:

AF XY:

0.438

AC XY:

32377

AN XY:

73982

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.424

Gnomad4 ASJ

AF:

0.633

Gnomad4 EAS

AF:

0.352

Gnomad4 SAS

AF:

0.430

Gnomad4 FIN

AF:

0.561

Gnomad4 NFE

AF:

0.563

Gnomad4 OTH

AF:

0.496

Alfa

AF:

0.480

Hom.:

2251

Bravo

AF:

0.422

Asia WGS

AF:

0.375

AC:

1296

AN:

3452

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.97

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over