chr3-195069856-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_152531.5(XXYLT1):c.1041G>A(p.Val347=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,614,146 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0095 ( 18 hom., cov: 33)
Exomes 𝑓: 0.00088 ( 18 hom. )
Consequence
XXYLT1
NM_152531.5 synonymous
NM_152531.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.321
Genes affected
XXYLT1 (HGNC:26639): (xyloside xylosyltransferase 1) Enables magnesium ion binding activity; manganese ion binding activity; and xylosyl alpha-1,3-xylosyltransferase activity. Involved in O-glycan processing. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 3-195069856-C-T is Benign according to our data. Variant chr3-195069856-C-T is described in ClinVar as [Benign]. Clinvar id is 780434.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.321 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00951 (1449/152302) while in subpopulation AFR AF= 0.0334 (1387/41562). AF 95% confidence interval is 0.0319. There are 18 homozygotes in gnomad4. There are 666 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XXYLT1 | NM_152531.5 | c.1041G>A | p.Val347= | synonymous_variant | 4/4 | ENST00000310380.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XXYLT1 | ENST00000310380.11 | c.1041G>A | p.Val347= | synonymous_variant | 4/4 | 1 | NM_152531.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00950 AC: 1445AN: 152184Hom.: 18 Cov.: 33
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GnomAD3 exomes AF: 0.00233 AC: 581AN: 249462Hom.: 7 AF XY: 0.00173 AC XY: 234AN XY: 135370
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GnomAD4 exome AF: 0.000879 AC: 1285AN: 1461844Hom.: 18 Cov.: 32 AF XY: 0.000752 AC XY: 547AN XY: 727228
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GnomAD4 genome ? AF: 0.00951 AC: 1449AN: 152302Hom.: 18 Cov.: 33 AF XY: 0.00894 AC XY: 666AN XY: 74470
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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 | Aug 27, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at