5-177600264-AGCG-A
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The ENST00000029410.10(B4GALT7):c.50+5_50+7delGCG variant causes a splice region, intron change. The variant allele was found at a frequency of 0.000000837 in 1,194,720 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000029410.10 splice_region, intron
Scores
Clinical Significance
Conservation
Publications
- 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
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
B4GALT7 | NM_007255.3 | c.50+12_50+14delCGG | intron_variant | Intron 1 of 5 | ENST00000029410.10 | NP_009186.1 | ||
B4GALT7 | XM_047416681.1 | c.-1061+12_-1061+14delCGG | intron_variant | Intron 1 of 6 | XP_047272637.1 | |||
B4GALT7 | XM_047416682.1 | c.-346+12_-346+14delCGG | intron_variant | Intron 1 of 6 | XP_047272638.1 | |||
B4GALT7 | XM_047416680.1 | c.-2221_-2219delGCG | upstream_gene_variant | XP_047272636.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD2 exomes AF: 0.0000291 AC: 1AN: 34406 AF XY: 0.0000474 show subpopulations
GnomAD4 exome AF: 8.37e-7 AC: 1AN: 1194720Hom.: 0 AF XY: 0.00000172 AC XY: 1AN XY: 581328 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at