rs117111131
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_194318.4(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
NM_194318.4 splice_polypyrimidine_tract, intron
NM_194318.4 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]
Genome browser will be placed here
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 | UniProt |
---|---|---|---|---|---|---|---|
B3GLCT | NM_194318.4 | c.271-12T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000343307.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B3GLCT | ENST00000343307.5 | c.271-12T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_194318.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0186 AC: 2814AN: 150988Hom.: 38 Cov.: 28
GnomAD3 genomes
?
AF:
AC:
2814
AN:
150988
Hom.:
Cov.:
28
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0214 AC: 5368AN: 251274Hom.: 88 AF XY: 0.0217 AC XY: 2948AN XY: 135796
GnomAD3 exomes
AF:
AC:
5368
AN:
251274
Hom.:
AF XY:
AC XY:
2948
AN XY:
135796
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0245 AC: 35404AN: 1446498Hom.: 541 Cov.: 31 AF XY: 0.0245 AC XY: 17636AN XY: 720648
GnomAD4 exome
AF:
AC:
35404
AN:
1446498
Hom.:
Cov.:
31
AF XY:
AC XY:
17636
AN XY:
720648
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0186 AC: 2812AN: 151098Hom.: 38 Cov.: 28 AF XY: 0.0175 AC XY: 1293AN XY: 73802
GnomAD4 genome
?
AF:
AC:
2812
AN:
151098
Hom.:
Cov.:
28
AF XY:
AC XY:
1293
AN XY:
73802
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
16
AN:
3478
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:6
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 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
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:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
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