rs199705453
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_022167.4(XYLT2):āc.2312A>Gā(p.Asn771Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000067 in 1,612,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. N771N) has been classified as Likely benign.
Frequency
Consequence
NM_022167.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XYLT2 | NM_022167.4 | c.2312A>G | p.Asn771Ser | missense_variant | 11/11 | ENST00000017003.7 | |
XYLT2 | XM_005257572.5 | c.2216A>G | p.Asn739Ser | missense_variant | 11/11 | ||
XYLT2 | XM_047436522.1 | c.1721A>G | p.Asn574Ser | missense_variant | 11/11 | ||
XYLT2 | NR_110010.2 | n.2131A>G | non_coding_transcript_exon_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XYLT2 | ENST00000017003.7 | c.2312A>G | p.Asn771Ser | missense_variant | 11/11 | 1 | NM_022167.4 | P1 | |
XYLT2 | ENST00000376550.7 | c.*196A>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/10 | 1 | ||||
XYLT2 | ENST00000507602.5 | c.1941+2753A>G | intron_variant | 2 | |||||
XYLT2 | ENST00000571021.1 | n.1028A>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000376 AC: 93AN: 247126Hom.: 0 AF XY: 0.000239 AC XY: 32AN XY: 133738
GnomAD4 exome AF: 0.0000692 AC: 101AN: 1459842Hom.: 0 Cov.: 29 AF XY: 0.0000551 AC XY: 40AN XY: 726022
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74454
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 11, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Nov 10, 2016 | - - |
Osteogenesis imperfecta Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Nov 17, 2020 | - - |
XYLT2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 29, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at