chr12-57626577-A-G
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001478.5(B4GALNT1):c.*167T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 768,280 control chromosomes in the GnomAD database, including 15,427 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.18 ( 2646 hom., cov: 32)
Exomes 𝑓: 0.20 ( 12781 hom. )
Consequence
B4GALNT1
NM_001478.5 3_prime_UTR
NM_001478.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.32
Genes affected
B4GALNT1 (HGNC:4117): (beta-1,4-N-acetyl-galactosaminyltransferase 1) GM2 and GD2 gangliosides are sialic acid-containing glycosphingolipids. GalNAc-T is the enzyme involved in the biosynthesis of G(M2) and G(D2) glycosphingolipids. GalNAc-T catalyzes the transfer of GalNAc into G(M3) and G(D3) by a beta-1,4 linkage, resulting in the synthesis of G(M2) and G(D2), respectively. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 12-57626577-A-G is Benign according to our data. Variant chr12-57626577-A-G is described in ClinVar as [Benign]. Clinvar id is 1242221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B4GALNT1 | NM_001478.5 | c.*167T>C | 3_prime_UTR_variant | 11/11 | ENST00000341156.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B4GALNT1 | ENST00000341156.9 | c.*167T>C | 3_prime_UTR_variant | 11/11 | 1 | NM_001478.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.180 AC: 27354AN: 152000Hom.: 2640 Cov.: 32
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GnomAD4 exome AF: 0.198 AC: 122128AN: 616162Hom.: 12781 Cov.: 8 AF XY: 0.194 AC XY: 62194AN XY: 320070
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GnomAD4 genome AF: 0.180 AC: 27375AN: 152118Hom.: 2646 Cov.: 32 AF XY: 0.178 AC XY: 13235AN XY: 74394
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at