5-177600264-AGCG-AGCGGCG
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The ENST00000029410.10(B4GALT7):c.50+4_50+5insGCG variant causes a splice region, intron change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000042 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
B4GALT7
ENST00000029410.10 splice_region, intron
ENST00000029410.10 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.04
Publications
0 publications found
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]
B4GALT7 Gene-Disease associations (from GenCC):
- Ehlers-Danlos syndrome, spondylodysplastic type, 1Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), PanelApp Australia, G2P, Ambry Genetics
- Ehlers-Danlos syndrome, spondylodysplastic typeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 5-177600264-A-AGCG is Benign according to our data. Variant chr5-177600264-A-AGCG is described in ClinVar as [Likely_benign]. Clinvar id is 1921513.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B4GALT7 | NM_007255.3 | c.50+12_50+14dupCGG | intron_variant | Intron 1 of 5 | ENST00000029410.10 | NP_009186.1 | ||
B4GALT7 | XM_047416681.1 | c.-1061+12_-1061+14dupCGG | intron_variant | Intron 1 of 6 | XP_047272637.1 | |||
B4GALT7 | XM_047416682.1 | c.-346+12_-346+14dupCGG | intron_variant | Intron 1 of 6 | XP_047272638.1 | |||
B4GALT7 | XM_047416680.1 | c.-2222_-2221insGCG | upstream_gene_variant | XP_047272636.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000418 AC: 5AN: 1194742Hom.: 0 Cov.: 30 AF XY: 0.00000516 AC XY: 3AN XY: 581340 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
5
AN:
1194742
Hom.:
Cov.:
30
AF XY:
AC XY:
3
AN XY:
581340
show subpopulations
African (AFR)
AF:
AC:
0
AN:
24264
American (AMR)
AF:
AC:
0
AN:
16204
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
18872
East Asian (EAS)
AF:
AC:
0
AN:
27180
South Asian (SAS)
AF:
AC:
0
AN:
53508
European-Finnish (FIN)
AF:
AC:
0
AN:
27714
Middle Eastern (MID)
AF:
AC:
0
AN:
3380
European-Non Finnish (NFE)
AF:
AC:
5
AN:
975600
Other (OTH)
AF:
AC:
0
AN:
48020
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.495
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Benign:1
Apr 16, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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