6-10528854-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_145649.5(GCNT2):c.-58T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 1,347,906 control chromosomes in the GnomAD database, including 4,143 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.082 ( 597 hom., cov: 32)
Exomes 𝑓: 0.073 ( 3546 hom. )
Consequence
GCNT2
NM_145649.5 5_prime_UTR
NM_145649.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.331
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=-0.76).
BP6
Variant 6-10528854-T-C is Benign according to our data. Variant chr6-10528854-T-C is described in ClinVar as [Benign]. Clinvar id is 1285722.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GCNT2 | NM_145649.5 | c.-58T>C | 5_prime_UTR_variant | 3/5 | ENST00000495262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GCNT2 | ENST00000495262.7 | c.-58T>C | 5_prime_UTR_variant | 3/5 | 2 | NM_145649.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0824 AC: 12517AN: 151890Hom.: 596 Cov.: 32
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GnomAD4 exome AF: 0.0729 AC: 87240AN: 1195898Hom.: 3546 Cov.: 17 AF XY: 0.0724 AC XY: 44014AN XY: 608158
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GnomAD4 genome AF: 0.0824 AC: 12520AN: 152008Hom.: 597 Cov.: 32 AF XY: 0.0799 AC XY: 5939AN XY: 74314
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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 | Oct 02, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at