9-76503084-T-C
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001490.5(GCNT1):āc.703T>Cā(p.Leu235Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,614,080 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.00083 ( 0 hom., cov: 32)
Exomes š: 0.0010 ( 19 hom. )
Consequence
GCNT1
NM_001490.5 synonymous
NM_001490.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.32
Genes affected
GCNT1 (HGNC:4203): (glucosaminyl (N-acetyl) transferase 1) This gene is a member of the beta-1,6-N-acetylglucosaminyltransferase gene family. It is essential to the formation of Gal beta 1-3(GlcNAc beta 1-6)GalNAc structures and the core 2 O-glycan branch. The gene coding this enzyme was originally mapped to 9q21, but was later localized to 9q13. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 9-76503084-T-C is Benign according to our data. Variant chr9-76503084-T-C is described in ClinVar as [Benign]. Clinvar id is 733713.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.32 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 19 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GCNT1 | ENST00000376730.5 | c.703T>C | p.Leu235Leu | synonymous_variant | 4/4 | 1 | NM_001490.5 | ENSP00000365920.4 | ||
GCNT1 | ENST00000442371.5 | c.703T>C | p.Leu235Leu | synonymous_variant | 3/3 | 1 | ENSP00000415454.1 | |||
GCNT1 | ENST00000444201.6 | c.703T>C | p.Leu235Leu | synonymous_variant | 3/3 | 1 | ENSP00000390703.2 | |||
GCNT1 | ENST00000648797.1 | n.142-12444T>C | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.000835 AC: 127AN: 152092Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00166 AC: 417AN: 251282Hom.: 5 AF XY: 0.00186 AC XY: 253AN XY: 135816
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GnomAD4 exome AF: 0.00102 AC: 1497AN: 1461870Hom.: 19 Cov.: 34 AF XY: 0.00117 AC XY: 850AN XY: 727234
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GnomAD4 genome AF: 0.000834 AC: 127AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000806 AC XY: 60AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 30, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at