rs16917929
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_024642.5(GALNT12):āc.897A>Gā(p.Gln299Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00685 in 1,613,826 control chromosomes in the GnomAD database, including 673 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.037 ( 362 hom., cov: 32)
Exomes š: 0.0037 ( 311 hom. )
Consequence
GALNT12
NM_024642.5 synonymous
NM_024642.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.562
Genes affected
GALNT12 (HGNC:19877): (polypeptide N-acetylgalactosaminyltransferase 12) This gene encodes a member of a family of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases, which catalyze the transfer of N-acetylgalactosamine (GalNAc) from UDP-GalNAc to a serine or threonine residue on a polypeptide acceptor in the initial step of O-linked protein glycosylation. Mutations in this gene are associated with an increased susceptibility to colorectal cancer.[provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 9-98831937-A-G is Benign according to our data. Variant chr9-98831937-A-G is described in ClinVar as [Benign]. Clinvar id is 416216.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-98831937-A-G is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=-0.562 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALNT12 | NM_024642.5 | c.897A>G | p.Gln299Gln | synonymous_variant | 4/10 | ENST00000375011.4 | NP_078918.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALNT12 | ENST00000375011.4 | c.897A>G | p.Gln299Gln | synonymous_variant | 4/10 | 1 | NM_024642.5 | ENSP00000364150.3 | ||
GALNT12 | ENST00000610463.1 | n.*328A>G | non_coding_transcript_exon_variant | 3/4 | 4 | ENSP00000477657.1 | ||||
GALNT12 | ENST00000610463.1 | n.*328A>G | 3_prime_UTR_variant | 3/4 | 4 | ENSP00000477657.1 |
Frequencies
GnomAD3 genomes AF: 0.0368 AC: 5598AN: 151970Hom.: 360 Cov.: 32
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GnomAD3 exomes AF: 0.00959 AC: 2409AN: 251078Hom.: 147 AF XY: 0.00686 AC XY: 931AN XY: 135712
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GnomAD4 exome AF: 0.00373 AC: 5450AN: 1461738Hom.: 311 Cov.: 32 AF XY: 0.00314 AC XY: 2285AN XY: 727164
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GnomAD4 genome AF: 0.0369 AC: 5608AN: 152088Hom.: 362 Cov.: 32 AF XY: 0.0359 AC XY: 2671AN XY: 74348
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 18, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | May 24, 2021 | - - |
GALNT12-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at