chr13-18724424-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000446657.2(GXYLT1P1):n.481C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0542 in 324,460 control chromosomes in the GnomAD database, including 34 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 0.059 ( 17 hom., cov: 49)
Exomes 𝑓: 0.050 ( 17 hom. )
Consequence
GXYLT1P1
ENST00000446657.2 non_coding_transcript_exon
ENST00000446657.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.16
Genes affected
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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=-0.78).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0866 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GXYLT1P1 | use as main transcript | n.18724424G>A | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GXYLT1P1 | ENST00000446657.2 | n.481C>T | non_coding_transcript_exon_variant | 1/1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0592 AC: 8989AN: 151900Hom.: 17 Cov.: 49
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GnomAD4 exome AF: 0.0498 AC: 8590AN: 172442Hom.: 17 Cov.: 0 AF XY: 0.0455 AC XY: 4565AN XY: 100244
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GnomAD4 genome AF: 0.0591 AC: 8991AN: 152018Hom.: 17 Cov.: 49 AF XY: 0.0578 AC XY: 4295AN XY: 74304
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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