Genetic Variant GLCE:c.*505A>T (chr15-69269749-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015554.3(GLCE):c.*505A>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 0.66 in 152,890 control chromosomes in the GnomAD database, including 35,548 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 0.66 ( 35321 hom., cov: 33)

Exomes 𝑓: 0.78 ( 227 hom. )

Consequence

GLCE
NM_015554.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.440

Publications

5 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLCE	NM_015554.3 link	c.*505A>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.*505A>T	3_prime_UTR_variant	Exon 5 of 5	1	NM_015554.3	ENSP00000261858.2	O94923
GLCE	ENST00000559420.2 link	c.*505A>T	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000454092.1	H0YNP1
PAQR5-DT	ENST00000746778.1 link	n.446-4316T>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.660

AC:

100288

AN:

152024

Hom.:

35318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.387

Gnomad AMI

AF:

0.769

Gnomad AMR

AF:

0.763

Gnomad ASJ

AF:

0.747

Gnomad EAS

AF:

0.746

Gnomad SAS

AF:

0.680

Gnomad FIN

AF:

0.783

Gnomad MID

AF:

0.718

Gnomad NFE

AF:

0.768

Gnomad OTH

AF:

0.697

GnomAD4 exome

AF:

0.779

AC:

583

AN:

748

Hom.:

227

Cov.:

AF XY:

0.797

AC XY:

341

AN XY:

428

show subpopulations

African (AFR)

AF:

0.200

AC:

AN:

American (AMR)

AF:

0.938

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.700

AC:

AN:

European-Finnish (FIN)

AF:

0.782

AC:

347

AN:

444

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.797

AC:

196

AN:

246

Other (OTH)

AF:

0.643

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.659

AC:

100321

AN:

152142

Hom.:

35321

Cov.:

AF XY:

0.663

AC XY:

49282

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.387

AC:

16060

AN:

41480

American (AMR)

AF:

0.763

AC:

11674

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.747

AC:

2593

AN:

3470

East Asian (EAS)

AF:

0.746

AC:

3865

AN:

5180

South Asian (SAS)

AF:

0.679

AC:

3272

AN:

4820

European-Finnish (FIN)

AF:

0.783

AC:

8284

AN:

10586

Middle Eastern (MID)

AF:

0.721

AC:

212

AN:

294

European-Non Finnish (NFE)

AF:

0.768

AC:

52204

AN:

68000

Other (OTH)

AF:

0.691

AC:

1457

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1562

3124

4685

6247

7809

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.706

Hom.:

4880

Bravo

AF:

0.648

Asia WGS

AF:

0.661

AC:

2292

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

5.4

(source)

DANN

Benign

0.82

PhyloP100

-0.44

Mutation Taster

=100/0

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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chr15-69269749-A-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over