rs7176782

Variant names:

• chr15-69185041-G-A
• rs7176782
• NM_015554.3:c.-105+24284G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-69185041-G-A
• chr15-69185041-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015554.3(GLCE):​c.-105+24284G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,080 control chromosomes in the GnomAD database, including 21,458 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 0.49 (21458 hom., cov: 33)
• Consequence: GLCE NM_015554.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.759
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GLCE	NM_015554.3	c.-105+24284G>A		intron_variant	Intron 1 of 4	ENST00000261858.7	NP_056369.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GLCE	ENST00000261858.7	c.-105+24284G>A		intron_variant	Intron 1 of 4	1	NM_015554.3	ENSP00000261858.2
GLCE	ENST00000559798.2	n.175-9395G>A		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74512 AN: 151964 Hom.: 21461 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.490 AC: 74498 AN: 152080 Hom.: 21458 Cov.: 33 AF XY: 0.495 AC XY: 36802 AN XY: 74338

African (AFR) AF: 0.162 AC: 6708 AN: 41484

American (AMR) AF: 0.631 AC: 9648 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2163 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2930 AN: 5178

South Asian (SAS) AF: 0.549 AC: 2650 AN: 4826

European-Finnish (FIN) AF: 0.624 AC: 6587 AN: 10556

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41951 AN: 67970

Other (OTH) AF: 0.521 AC: 1099 AN: 2110

Alfa AF: 0.579 Hom.: 33120

Bravo AF: 0.478

Asia WGS AF: 0.479 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.54
PhyloP100		-0.76
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: rs7176782; hg19: chr15-69477380; COSMIC: COSV55944890;