NM_015554.3:c.-13-6086A>G

Variant names:

• chr15-69249708-A-G
• rs17360351
• NM_015554.3:c.-13-6086A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GLCE	NM_015554.3	c.-13-6086A>G		intron_variant	Intron 2 of 4	ENST00000261858.7	NP_056369.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLCE	ENST00000261858.7	c.-13-6086A>G		intron_variant	Intron 2 of 4	1	NM_015554.3	ENSP00000261858.2

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

African (AFR) AF: 0.0145 AC: 604 AN: 41552

American (AMR) AF: 0.0727 AC: 1111 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 343 AN: 3470

East Asian (EAS) AF: 0.104 AC: 539 AN: 5168

South Asian (SAS) AF: 0.0348 AC: 168 AN: 4824

European-Finnish (FIN) AF: 0.0670 AC: 711 AN: 10606

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0783 AC: 5327 AN: 68000

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0651 Hom.: 324

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
PhyloP100		0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17360351; hg19: chr15-69542047;