chr12-42109703-T-TA
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_173601.2(GXYLT1):c.487-13_487-12insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000403 in 1,240,524 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000040 ( 0 hom. )
Consequence
GXYLT1
NM_173601.2 splice_polypyrimidine_tract, intron
NM_173601.2 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.696
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 12-42109703-T-TA is Benign according to our data. Variant chr12-42109703-T-TA is described in ClinVar as [Benign]. Clinvar id is 2776143.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.487-13_487-12insT | splice_polypyrimidine_tract_variant, intron_variant | ENST00000398675.8 | |||
GXYLT1 | NM_001099650.2 | c.394-13_394-12insT | splice_polypyrimidine_tract_variant, intron_variant | ||||
GXYLT1 | XM_017019211.1 | c.142-13_142-12insT | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GXYLT1 | ENST00000398675.8 | c.487-13_487-12insT | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_173601.2 | P4 | |||
GXYLT1 | ENST00000280876.6 | c.394-13_394-12insT | splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome AF: 0.00000403 AC: 5AN: 1240524Hom.: 0 Cov.: 21 AF XY: 0.00000642 AC XY: 4AN XY: 623342
GnomAD4 exome
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5
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1240524
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21
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4
AN XY:
623342
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Computational scores
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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