15-69256054-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015554.3(GLCE):c.248A>G(p.Lys83Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00216 in 1,614,056 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 22 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 16 hom. )
Consequence
GLCE
NM_015554.3 missense
NM_015554.3 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 3.96
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.002390802).
BP6
?
Variant 15-69256054-A-G is Benign according to our data. Variant chr15-69256054-A-G is described in ClinVar as [Benign]. Clinvar id is 787120.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00999 (1521/152242) while in subpopulation AFR AF= 0.0324 (1344/41542). AF 95% confidence interval is 0.0309. There are 22 homozygotes in gnomad4. There are 719 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 22 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLCE | NM_015554.3 | c.248A>G | p.Lys83Arg | missense_variant | 3/5 | ENST00000261858.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLCE | ENST00000261858.7 | c.248A>G | p.Lys83Arg | missense_variant | 3/5 | 1 | NM_015554.3 | P1 | |
GLCE | ENST00000559420.2 | c.56A>G | p.Lys19Arg | missense_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0100 AC: 1521AN: 152124Hom.: 22 Cov.: 32
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GnomAD3 exomes AF: 0.00269 AC: 675AN: 251128Hom.: 6 AF XY: 0.00217 AC XY: 294AN XY: 135700
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GnomAD4 exome AF: 0.00134 AC: 1963AN: 1461814Hom.: 16 Cov.: 33 AF XY: 0.00121 AC XY: 882AN XY: 727214
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GnomAD4 genome ? AF: 0.00999 AC: 1521AN: 152242Hom.: 22 Cov.: 32 AF XY: 0.00966 AC XY: 719AN XY: 74452
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ESP6500AA
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 16, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at