12-42144467-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_173601.2(GXYLT1):c.180C>T(p.Ala60=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000020 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GXYLT1
NM_173601.2 synonymous
NM_173601.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0620
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 12-42144467-G-A is Benign according to our data. Variant chr12-42144467-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2642890.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.062 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| GXYLT1 | NM_173601.2 | c.180C>T | p.Ala60= | synonymous_variant | 1/8 | ENST00000398675.8 | |
| GXYLT1 | NM_001099650.2 | c.180C>T | p.Ala60= | synonymous_variant | 1/7 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GXYLT1 | ENST00000398675.8 | c.180C>T | p.Ala60= | synonymous_variant | 1/8 | 1 | NM_173601.2 | P4 | |
| GXYLT1 | ENST00000280876.6 | c.180C>T | p.Ala60= | synonymous_variant | 1/7 | 1 | A1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD3 exomes AF: 0.0000620 AC: 1AN: 16130Hom.: 0 AF XY: 0.0000934 AC XY: 1AN XY: 10710
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000202 AC: 2AN: 990842Hom.: 0 Cov.: 32 AF XY: 0.00000425 AC XY: 2AN XY: 470758
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome
GnomAD4 genome
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31
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 | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | GXYLT1: BP4, BP7 - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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