5-177600185-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_007255.3(B4GALT7):c.-26C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00351 in 1,342,070 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0021 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0037 ( 10 hom. )
Consequence
B4GALT7
NM_007255.3 5_prime_UTR
NM_007255.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.417
Genes affected
B4GALT7 (HGNC:930): (beta-1,4-galactosyltransferase 7) This gene is a member of the beta-1,4-galactosyltransferase (beta4GalT) family. Family members encode type II membrane-bound glycoproteins that appear to have exclusive specificity for the donor substrate UDP-galactose. Each beta4GalT member has a distinct function in the biosynthesis of different glycoconjugates and saccharide structures. As type II membrane proteins, they have an N-terminal hydrophobic signal sequence that directs the protein to the Golgi apparatus which then remains uncleaved to function as a transmembrane anchor. The enzyme encoded by this gene attaches the first galactose in the common carbohydrate-protein linkage (GlcA-beta1,3-Gal-beta1,3-Gal-beta1,4-Xyl-beta1-O-Ser) found in proteoglycans. This enzyme differs from other beta4GalTs because it lacks the conserved Cys residues found in beta4GalT1-beta4GalT6 and it is located in cis-Golgi instead of trans-Golgi. Mutations in this gene have been associated with the progeroid form of Ehlers-Danlos syndrome. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
Variant 5-177600185-C-T is Benign according to our data. Variant chr5-177600185-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 384811.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00212 (321/151728) while in subpopulation NFE AF= 0.00351 (238/67842). AF 95% confidence interval is 0.00314. There are 1 homozygotes in gnomad4. There are 165 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 |
---|---|---|---|---|---|---|---|
B4GALT7 | NM_007255.3 | c.-26C>T | 5_prime_UTR_variant | 1/6 | ENST00000029410.10 | ||
B4GALT7 | XM_047416681.1 | c.-1136C>T | 5_prime_UTR_variant | 1/7 | |||
B4GALT7 | XM_047416682.1 | c.-421C>T | 5_prime_UTR_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B4GALT7 | ENST00000029410.10 | c.-26C>T | 5_prime_UTR_variant | 1/6 | 1 | NM_007255.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00212 AC: 321AN: 151620Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00161 AC: 71AN: 43976Hom.: 0 AF XY: 0.00195 AC XY: 51AN XY: 26202
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GnomAD4 exome AF: 0.00369 AC: 4387AN: 1190342Hom.: 10 Cov.: 30 AF XY: 0.00364 AC XY: 2114AN XY: 580118
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 30, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at