15-69249708-A-G

Position:

• chr15-69249708-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015554.3(GLCE):​c.-13-6086A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 152,230 control chromosomes in the GnomAD database, including 358 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 0.060 (358 hom., cov: 32)
• Consequence: GLCE NM_015554.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.097 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GLCE	NM_015554.3	c.-13-6086A>G		intron_variant		ENST00000261858.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GLCE	ENST00000261858.7	c.-13-6086A>G		intron_variant		1	NM_015554.3	P1

Frequencies

GnomAD3 genomes AF: 0.0601 AC: 9140 AN: 152112 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0348

Gnomad FIN AF: 0.0670

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.0693

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0601 AC: 9146 AN: 152230 Hom.: 358 Cov.: 32 AF XY: 0.0594 AC XY: 4420 AN XY: 74450

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0727

Gnomad4 ASJ AF: 0.0988

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0348

Gnomad4 FIN AF: 0.0670

Gnomad4 NFE AF: 0.0783

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0708 Hom.: 290

Bravo AF: 0.0579

Asia WGS AF: 0.0610 AC: 212 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.81

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: rs17360351; hg19: chr15-69542047;