chr12-42109700-AT-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_173601.2(GXYLT1):c.487-10del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00083 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
GXYLT1
NM_173601.2 splice_polypyrimidine_tract, intron
NM_173601.2 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.564
Genes affected
GXYLT1 (HGNC:27482): (glucoside xylosyltransferase 1) GXYLT1 is a xylosyltransferase (EC 2.4.2.-) that adds the first xylose to O-glucose-modified residues in the epidermal growth factor (EGF; MIM 131530) repeats of proteins such as NOTCH1 (MIM 190198) (Sethi et al., 2010 [PubMed 19940119]).[supplied by OMIM, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant 12-42109700-AT-A is Benign according to our data. Variant chr12-42109700-AT-A is described in ClinVar as [Likely_benign]. Clinvar id is 2723349.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GXYLT1 | NM_173601.2 | c.487-10del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000398675.8 | |||
GXYLT1 | NM_001099650.2 | c.394-10del | splice_polypyrimidine_tract_variant, intron_variant | ||||
GXYLT1 | XM_017019211.1 | c.142-10del | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GXYLT1 | ENST00000398675.8 | c.487-10del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_173601.2 | P4 | |||
GXYLT1 | ENST00000280876.6 | c.394-10del | splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 2AN: 148240Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome AF: 0.000835 AC: 1056AN: 1264888Hom.: 1 Cov.: 20 AF XY: 0.000780 AC XY: 495AN XY: 634438
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000135 AC: 2AN: 148240Hom.: 0 Cov.: 32 AF XY: 0.0000277 AC XY: 2AN XY: 72238
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at