rs1564892
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_047429629.1(GLT8D2):c.-2233T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,042 control chromosomes in the GnomAD database, including 11,552 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 0.36 ( 11552 hom., cov: 33)
Consequence
GLT8D2
XM_047429629.1 5_prime_UTR
XM_047429629.1 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.77
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLT8D2 | XM_047429629.1 | c.-2233T>C | 5_prime_UTR_variant | 2/12 | |||
GLT8D2 | XM_047429630.1 | c.-2303T>C | 5_prime_UTR_variant | 2/13 | |||
GLT8D2 | XM_047429631.1 | c.-2098T>C | 5_prime_UTR_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT8D2 | ENST00000548660.5 | c.-422-1676T>C | intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.357 AC: 54163AN: 151924Hom.: 11528 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.357 AC: 54233AN: 152042Hom.: 11552 Cov.: 33 AF XY: 0.359 AC XY: 26699AN XY: 74322
GnomAD4 genome
?
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26699
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74322
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at