chr1-1232256-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_080605.4(B3GALT6):c.-23G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 980,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
B3GALT6
NM_080605.4 5_prime_UTR
NM_080605.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.114
Genes affected
B3GALT6 (HGNC:17978): (beta-1,3-galactosyltransferase 6) The enzyme encoded by this intronless gene is a beta-1,3-galactosyltransferase found in the medial Golgi apparatus, where it catalyzes the transfer of galactose from UDP-galactose to substrates containing a terminal beta-linked galactose moiety. The encoded enzyme has a particular affinity for galactose-beta-1,4-xylose found in the linker region of glycosamines. This enzyme is required for glycosaminoglycan synthesis. [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 1-1232256-G-A is Benign according to our data. Variant chr1-1232256-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 390144.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B3GALT6 | NM_080605.4 | c.-23G>A | 5_prime_UTR_variant | 1/1 | ENST00000379198.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B3GALT6 | ENST00000379198.5 | c.-23G>A | 5_prime_UTR_variant | 1/1 | NM_080605.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000219 AC: 32AN: 146362Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000144 AC: 120AN: 834444Hom.: 0 Cov.: 29 AF XY: 0.000153 AC XY: 59AN XY: 385440
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GnomAD4 genome AF: 0.000218 AC: 32AN: 146468Hom.: 0 Cov.: 33 AF XY: 0.000210 AC XY: 15AN XY: 71330
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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 | Oct 20, 2016 | 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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Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at