chr19-17807939-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_014256.4(B3GNT3):c.132C>T(p.Pro44=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,613,396 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0058 ( 7 hom., cov: 30)
Exomes 𝑓: 0.00062 ( 10 hom. )
Consequence
B3GNT3
NM_014256.4 synonymous
NM_014256.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.16
Genes affected
B3GNT3 (HGNC:13528): (UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3) This gene encodes a member of the beta-1,3-N-acetylglucosaminyltransferase family. This enzyme is a type II transmembrane protein and contains a signal anchor that is not cleaved. It prefers the substrates of lacto-N-tetraose and lacto-N-neotetraose, and is involved in the biosynthesis of poly-N-acetyllactosamine chains and the biosynthesis of the backbone structure of dimeric sialyl Lewis a. It plays dominant roles in L-selectin ligand biosynthesis, lymphocyte homing and lymphocyte trafficking. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant 19-17807939-C-T is Benign according to our data. Variant chr19-17807939-C-T is described in ClinVar as [Benign]. Clinvar id is 769962.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.16 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00578 (880/152202) while in subpopulation AFR AF= 0.0205 (851/41520). AF 95% confidence interval is 0.0194. There are 7 homozygotes in gnomad4. There are 422 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B3GNT3 | NM_014256.4 | c.132C>T | p.Pro44= | synonymous_variant | 2/3 | ENST00000318683.7 | NP_055071.2 | |
B3GNT3 | XM_011527626.3 | c.132C>T | p.Pro44= | synonymous_variant | 2/3 | XP_011525928.1 | ||
B3GNT3 | XM_047438042.1 | c.132C>T | p.Pro44= | synonymous_variant | 2/3 | XP_047293998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
B3GNT3 | ENST00000318683.7 | c.132C>T | p.Pro44= | synonymous_variant | 2/3 | 1 | NM_014256.4 | ENSP00000321874 | P1 | |
B3GNT3 | ENST00000595387.1 | c.132C>T | p.Pro44= | synonymous_variant | 2/3 | 1 | ENSP00000472638 | P1 | ||
B3GNT3 | ENST00000599265.5 | c.132C>T | p.Pro44= | synonymous_variant | 2/3 | 3 | ENSP00000471733 | |||
B3GNT3 | ENST00000600777.1 | c.132C>T | p.Pro44= | synonymous_variant | 2/2 | 3 | ENSP00000468914 |
Frequencies
GnomAD3 genomes AF: 0.00575 AC: 875AN: 152084Hom.: 7 Cov.: 30
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GnomAD3 exomes AF: 0.00167 AC: 414AN: 248140Hom.: 2 AF XY: 0.00119 AC XY: 160AN XY: 134898
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GnomAD4 exome AF: 0.000625 AC: 913AN: 1461194Hom.: 10 Cov.: 30 AF XY: 0.000537 AC XY: 390AN XY: 726916
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GnomAD4 genome AF: 0.00578 AC: 880AN: 152202Hom.: 7 Cov.: 30 AF XY: 0.00567 AC XY: 422AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2018 | - - |
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