17-50360095-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_022167.4(XYLT2):c.2402C>G(p.Thr801Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 1,613,648 control chromosomes in the GnomAD database, including 112,784 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T801I) has been classified as Uncertain significance.
Frequency
Consequence
NM_022167.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XYLT2 | NM_022167.4 | c.2402C>G | p.Thr801Arg | missense_variant | 11/11 | ENST00000017003.7 | |
XYLT2 | XM_005257572.5 | c.2306C>G | p.Thr769Arg | missense_variant | 11/11 | ||
XYLT2 | XM_047436522.1 | c.1811C>G | p.Thr604Arg | missense_variant | 11/11 | ||
XYLT2 | NR_110010.2 | n.2221C>G | non_coding_transcript_exon_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XYLT2 | ENST00000017003.7 | c.2402C>G | p.Thr801Arg | missense_variant | 11/11 | 1 | NM_022167.4 | P1 | |
XYLT2 | ENST00000376550.7 | c.*286C>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/10 | 1 | ||||
XYLT2 | ENST00000507602.5 | c.1941+2843C>G | intron_variant | 2 | |||||
XYLT2 | ENST00000571021.1 | n.1118C>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.330 AC: 50095AN: 152004Hom.: 8956 Cov.: 33
GnomAD3 exomes AF: 0.330 AC: 82635AN: 250440Hom.: 15108 AF XY: 0.340 AC XY: 46104AN XY: 135474
GnomAD4 exome AF: 0.371 AC: 541626AN: 1461526Hom.: 103819 Cov.: 67 AF XY: 0.372 AC XY: 270374AN XY: 727052
GnomAD4 genome ? AF: 0.329 AC: 50123AN: 152122Hom.: 8965 Cov.: 33 AF XY: 0.330 AC XY: 24526AN XY: 74386
ClinVar
Submissions by phenotype
Spondylo-ocular syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 25, 2020 | This variant is associated with the following publications: (PMID: 16571645) - |
Osteogenesis imperfecta Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jul 16, 2022 | - - |
Pseudoxanthoma elasticum, modifier of severity of Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Sep 01, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at