chr6-10530003-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_145649.5(GCNT2):c.925+167A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 630,822 control chromosomes in the GnomAD database, including 193 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.019 ( 44 hom., cov: 32)
Exomes 𝑓: 0.022 ( 149 hom. )
Consequence
GCNT2
NM_145649.5 intron
NM_145649.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.521
Genes affected
GCNT2 (HGNC:4204): (glucosaminyl (N-acetyl) transferase 2 (I blood group)) This gene encodes the enzyme responsible for formation of the blood group I antigen. The i and I antigens are distinguished by linear and branched poly-N-acetyllactosaminoglycans, respectively. The encoded protein is the I-branching enzyme, a beta-1,6-N-acetylglucosaminyltransferase responsible for the conversion of fetal i antigen to adult I antigen in erythrocytes during embryonic development. Mutations in this gene have been associated with adult i blood group phenotype. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 6-10530003-A-T is Benign according to our data. Variant chr6-10530003-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 1215107.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0191 (2907/152320) while in subpopulation NFE AF= 0.0285 (1938/68032). AF 95% confidence interval is 0.0274. There are 44 homozygotes in gnomad4. There are 1397 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 44 BG,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCNT2 | NM_145649.5 | c.925+167A>T | intron_variant | ENST00000495262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCNT2 | ENST00000495262.7 | c.925+167A>T | intron_variant | 2 | NM_145649.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0191 AC: 2909AN: 152202Hom.: 44 Cov.: 32
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GnomAD4 exome AF: 0.0222 AC: 10633AN: 478502Hom.: 149 Cov.: 5 AF XY: 0.0213 AC XY: 5394AN XY: 253614
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GnomAD4 genome ? AF: 0.0191 AC: 2907AN: 152320Hom.: 44 Cov.: 32 AF XY: 0.0188 AC XY: 1397AN XY: 74482
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 24, 2019 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at