17-50346197-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_022167.4(XYLT2):c.57C>A(p.Ala19Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000309 in 1,295,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A19A) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000026 ( 0 hom. )
Consequence
XYLT2
NM_022167.4 synonymous
NM_022167.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.14
Publications
0 publications found
Genes affected
XYLT2 (HGNC:15517): (xylosyltransferase 2) The protein encoded by this gene is an isoform of xylosyltransferase, which belongs to a family of glycosyltransferases. This enzyme transfers xylose from UDP-xylose to specific serine residues of the core protein and initiates the biosynthesis of glycosaminoglycan chains in proteoglycans including chondroitin sulfate, heparan sulfate, heparin and dermatan sulfate. The enzyme activity, which is increased in scleroderma patients, is a diagnostic marker for the determination of sclerotic activity in systemic sclerosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2013]
XYLT2 Gene-Disease associations (from GenCC):
- spondylo-ocular syndromeInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP7
Synonymous conserved (PhyloP=1.14 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_022167.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| XYLT2 | NM_022167.4 | MANE Select | c.57C>A | p.Ala19Ala | synonymous | Exon 1 of 11 | NP_071450.2 | Q9H1B5-1 | |
| XYLT2 | NR_110010.2 | n.72C>A | non_coding_transcript_exon | Exon 1 of 10 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| XYLT2 | ENST00000017003.7 | TSL:1 MANE Select | c.57C>A | p.Ala19Ala | synonymous | Exon 1 of 11 | ENSP00000017003.2 | Q9H1B5-1 | |
| XYLT2 | ENST00000376550.7 | TSL:1 | n.57C>A | non_coding_transcript_exon | Exon 1 of 10 | ENSP00000365733.3 | A0A0C4DFW8 | ||
| XYLT2 | ENST00000854775.1 | c.57C>A | p.Ala19Ala | synonymous | Exon 1 of 11 | ENSP00000524834.1 |
Frequencies
GnomAD3 genomes 0.00000675 AC: 1AN: 148042Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
148042
Hom.:
Cov.:
32
Gnomad AFR
AF:
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Gnomad FIN
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.0000117 AC: 1AN: 85724 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
85724
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.00000262 AC: 3AN: 1147124Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 565552 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1147124
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
565552
show subpopulations
African (AFR)
AF:
AC:
0
AN:
22118
American (AMR)
AF:
AC:
0
AN:
20466
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
16796
East Asian (EAS)
AF:
AC:
0
AN:
17494
South Asian (SAS)
AF:
AC:
0
AN:
64748
European-Finnish (FIN)
AF:
AC:
2
AN:
31220
Middle Eastern (MID)
AF:
AC:
0
AN:
3214
European-Non Finnish (NFE)
AF:
AC:
1
AN:
929092
Other (OTH)
AF:
AC:
0
AN:
41976
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.542
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000675 AC: 1AN: 148042Hom.: 0 Cov.: 32 AF XY: 0.0000139 AC XY: 1AN XY: 72090 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
148042
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
72090
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41088
American (AMR)
AF:
AC:
0
AN:
14878
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3406
East Asian (EAS)
AF:
AC:
0
AN:
5152
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
1
AN:
8990
Middle Eastern (MID)
AF:
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66430
Other (OTH)
AF:
AC:
0
AN:
2042
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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