rs117111131
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000343307.5(B3GLCT):c.271-12T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0239 in 1,597,596 control chromosomes in the GnomAD database, including 579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.019 ( 38 hom., cov: 28)
Exomes 𝑓: 0.024 ( 541 hom. )
Consequence
B3GLCT
ENST00000343307.5 splice_polypyrimidine_tract, intron
ENST00000343307.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00008837
2
Clinical Significance
Conservation
PhyloP100: -0.256
Genes affected
B3GLCT (HGNC:20207): (beta 3-glucosyltransferase) The protein encoded by this gene is a beta-1,3-glucosyltransferase that transfers glucose to O-linked fucosylglycans on thrombospondin type-1 repeats (TSRs) of several proteins. The encoded protein is a type II membrane protein. Defects in this gene are a cause of Peters-plus syndrome (PPS).[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 13-31247011-T-C is Benign according to our data. Variant chr13-31247011-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 96625.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr13-31247011-T-C is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0186 (2812/151098) while in subpopulation NFE AF= 0.0263 (1787/67856). AF 95% confidence interval is 0.0253. There are 38 homozygotes in gnomad4. There are 1293 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 38 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GLCT | NM_194318.4 | c.271-12T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000343307.5 | NP_919299.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
B3GLCT | ENST00000343307.5 | c.271-12T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_194318.4 | ENSP00000343002 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0186 AC: 2814AN: 150988Hom.: 38 Cov.: 28
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GnomAD3 exomes AF: 0.0214 AC: 5368AN: 251274Hom.: 88 AF XY: 0.0217 AC XY: 2948AN XY: 135796
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GnomAD4 exome AF: 0.0245 AC: 35404AN: 1446498Hom.: 541 Cov.: 31 AF XY: 0.0245 AC XY: 17636AN XY: 720648
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GnomAD4 genome AF: 0.0186 AC: 2812AN: 151098Hom.: 38 Cov.: 28 AF XY: 0.0175 AC XY: 1293AN XY: 73802
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Peters plus syndrome Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 18, 2013 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at