rs139287952
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_006876.3(B4GAT1):c.1161G>A(p.Glu387=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000181 in 1,614,126 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00097 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000099 ( 1 hom. )
Consequence
B4GAT1
NM_006876.3 synonymous
NM_006876.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0620
Genes affected
B4GAT1 (HGNC:15685): (beta-1,4-glucuronyltransferase 1) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein. It is essential for the synthesis of poly-N-acetyllactosamine, a determinant for the blood group i antigen. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 11-66346136-C-T is Benign according to our data. Variant chr11-66346136-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 474248.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=0.062 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000972 (148/152244) while in subpopulation AFR AF= 0.00344 (143/41548). AF 95% confidence interval is 0.00298. There are 0 homozygotes in gnomad4. There are 80 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B4GAT1 | NM_006876.3 | c.1161G>A | p.Glu387= | synonymous_variant | 2/2 | ENST00000311181.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B4GAT1 | ENST00000311181.5 | c.1161G>A | p.Glu387= | synonymous_variant | 2/2 | 1 | NM_006876.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000966 AC: 147AN: 152126Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000248 AC: 62AN: 249854Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 135216
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GnomAD4 exome AF: 0.0000985 AC: 144AN: 1461882Hom.: 1 Cov.: 31 AF XY: 0.0000866 AC XY: 63AN XY: 727244
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GnomAD4 genome ? AF: 0.000972 AC: 148AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.00107 AC XY: 80AN XY: 74446
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
B4GAT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 28, 2019 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 25, 2019 | - - |
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at