Variant 15-69272004-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_015554.3(GLCE):c.*2760C>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 0.517 in 152,442 control chromosomes in the GnomAD database, including 23,675 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 0.52 ( 23586 hom., cov: 32)

Exomes 𝑓: 0.64 ( 89 hom. )

Consequence

GLCE
NM_015554.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.17

Variant links:

Genes affected

GLCE (HGNC:17855): (glucuronic acid epimerase) Enables calcium ion binding activity; heparosan-N-sulfate-glucuronate 5-epimerase activity; and protein homodimerization activity. Involved in heparan sulfate proteoglycan biosynthetic process. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

GLCE links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLCE	NM_015554.3 linkuse as main transcript	c.*2760C>T		3_prime_UTR_variant	5/5	ENST00000261858.7	NP_056369.1	O94923

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLCE	ENST00000261858.7 linkuse as main transcript	c.*2760C>T		3_prime_UTR_variant	5/5	1	NM_015554.3	ENSP00000261858.2		O94923
GLCE	ENST00000559420.2 linkuse as main transcript	c.*2760C>T		3_prime_UTR_variant	3/3	1		ENSP00000454092.1		H0YNP1

Frequencies

GnomAD3 genomes

AF:

0.517

AC:

78523

AN:

151892

Hom.:

23584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.669

Gnomad AMR

AF:

0.657

Gnomad ASJ

AF:

0.663

Gnomad EAS

AF:

0.588

Gnomad SAS

AF:

0.572

Gnomad FIN

AF:

0.649

Gnomad MID

AF:

0.636

Gnomad NFE

AF:

0.646

Gnomad OTH

AF:

0.558

GnomAD4 exome

AF:

0.644

AC:

278

AN:

432

Hom.:

Cov.:

AF XY:

0.669

AC XY:

174

AN XY:

260

show subpopulations

Gnomad4 FIN exome

AF:

0.646

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.517

AC:

78523

AN:

152010

Hom.:

23586

Cov.:

AF XY:

0.521

AC XY:

38737

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.185

Gnomad4 AMR

AF:

0.658

Gnomad4 ASJ

AF:

0.663

Gnomad4 EAS

AF:

0.588

Gnomad4 SAS

AF:

0.571

Gnomad4 FIN

AF:

0.649

Gnomad4 NFE

AF:

0.646

Gnomad4 OTH

AF:

0.550

Alfa

AF:

0.565

Hom.:

5757

Bravo

AF:

0.504

Asia WGS

AF:

0.499

AC:

1732

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over