chr12-104015060-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001384711.1(GLT8D2):āc.65T>Cā(p.Ile22Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000311 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00019 ( 0 hom., cov: 32)
Exomes š: 0.00032 ( 0 hom. )
Consequence
GLT8D2
NM_001384711.1 missense
NM_001384711.1 missense
Scores
12
6
Clinical Significance
Conservation
PhyloP100: 4.80
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.65T>C | p.Ile22Thr | missense_variant | 4/11 | ENST00000360814.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT8D2 | ENST00000360814.9 | c.65T>C | p.Ile22Thr | missense_variant | 4/11 | 1 | NM_001384711.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152168Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000239 AC: 60AN: 251304Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135812
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GnomAD4 exome AF: 0.000324 AC: 473AN: 1461706Hom.: 0 Cov.: 30 AF XY: 0.000274 AC XY: 199AN XY: 727168
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GnomAD4 genome AF: 0.000191 AC: 29AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74334
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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 | Feb 26, 2024 | The c.65T>C (p.I22T) alteration is located in exon 4 (coding exon 2) of the GLT8D2 gene. This alteration results from a T to C substitution at nucleotide position 65, causing the isoleucine (I) at amino acid position 22 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
P;P;P;.
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