12-103993504-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001384711.1(GLT8D2):c.768G>C(p.Glu256Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,557,666 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000019 ( 1 hom. )
Consequence
GLT8D2
NM_001384711.1 missense, splice_region
NM_001384711.1 missense, splice_region
Scores
2
15
Splicing: ADA: 0.8636
1
1
Clinical Significance
Conservation
PhyloP100: 0.423
Genes affected
GLT8D2 (HGNC:24890): (glycosyltransferase 8 domain containing 2) Predicted to enable glycosyltransferase activity. 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 Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLT8D2 | NM_001384711.1 | c.768G>C | p.Glu256Asp | missense_variant, splice_region_variant | 10/11 | ENST00000360814.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT8D2 | ENST00000360814.9 | c.768G>C | p.Glu256Asp | missense_variant, splice_region_variant | 10/11 | 1 | NM_001384711.1 | P1 | |
GLT8D2 | ENST00000546436.5 | c.768G>C | p.Glu256Asp | missense_variant, splice_region_variant | 9/10 | 5 | P1 | ||
GLT8D2 | ENST00000548660.5 | c.768G>C | p.Glu256Asp | missense_variant, splice_region_variant | 10/11 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152132Hom.: 0 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000678 AC: 14AN: 206566Hom.: 0 AF XY: 0.0000446 AC XY: 5AN XY: 112232
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GnomAD4 exome AF: 0.0000192 AC: 27AN: 1405416Hom.: 1 Cov.: 27 AF XY: 0.0000201 AC XY: 14AN XY: 696354
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GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74444
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2021 | The c.768G>C (p.E256D) alteration is located in exon 10 (coding exon 8) of the GLT8D2 gene. This alteration results from a G to C substitution at nucleotide position 768, causing the glutamic acid (E) at amino acid position 256 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
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;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
D;D;D
Sift4G
Benign
T;T;T
Polyphen
P;P;P
Vest4
MutPred
Gain of catalytic residue at Y260 (P = 0.0062);Gain of catalytic residue at Y260 (P = 0.0062);Gain of catalytic residue at Y260 (P = 0.0062);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 0
Find out detailed SpliceAI scores and Pangolin per-transcript scores at