Genetic Variant NM_015554.3:c.*2760C>T (chr15-69272004-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

6 publications found

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:

PAQR5-DT (HGNC:55353): (PAQR5 divergent transcript)

PAQR5-DT links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GLCE	NM_015554.3 link	c.*2760C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000261858.7	NP_056369.1	O94923

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GLCE	ENST00000261858.7 link	c.*2760C>T	3_prime_UTR_variant	Exon 5 of 5	1	NM_015554.3	ENSP00000261858.2	O94923
GLCE	ENST00000559420.2 link	c.*2760C>T	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000454092.1	H0YNP1
PAQR5-DT	ENST00000746778.1 link	n.446-6571G>A	intron_variant	Intron 2 of 3

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

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.646

AC:

275

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.517

AC:

78523

AN:

152010

Hom.:

23586

Cov.:

AF XY:

0.521

AC XY:

38737

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.185

AC:

7687

AN:

41458

American (AMR)

AF:

0.658

AC:

10045

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.663

AC:

2301

AN:

3472

East Asian (EAS)

AF:

0.588

AC:

3035

AN:

5164

South Asian (SAS)

AF:

0.571

AC:

2750

AN:

4818

European-Finnish (FIN)

AF:

0.649

AC:

6846

AN:

10542

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.646

AC:

43904

AN:

67976

Other (OTH)

AF:

0.550

AC:

1158

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1640

3281

4921

6562

8202

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.569

Hom.:

10391

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

(source)

DANN

Benign

0.84

PhyloP100

2.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over