rs4621175
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004482.4(GALNT3):c.-109+1733T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 152,120 control chromosomes in the GnomAD database, including 49,811 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.80 ( 49811 hom., cov: 33)
Consequence
GALNT3
NM_004482.4 intron
NM_004482.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.72
Genes affected
GALNT3 (HGNC:4125): (polypeptide N-acetylgalactosaminyltransferase 3) This gene encodes UDP-GalNAc transferase 3, a member of the GalNAc-transferases family. This family transfers an N-acetyl galactosamine to the hydroxyl group of a serine or threonine residue in the first step of O-linked oligosaccharide biosynthesis. Individual GalNAc-transferases have distinct activities and initiation of O-glycosylation is regulated by a repertoire of GalNAc-transferases. The protein encoded by this gene is highly homologous to other family members, however the enzymes have different substrate specificities. [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=-0.83).
BP6
Variant 2-165792282-A-C is Benign according to our data. Variant chr2-165792282-A-C is described in ClinVar as [Benign]. Clinvar id is 1232432.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GALNT3 | NM_004482.4 | c.-109+1733T>G | intron_variant | Intron 1 of 10 | ENST00000392701.8 | NP_004473.2 | ||
| GALNT3 | XM_011510929.2 | c.-109+2207T>G | intron_variant | Intron 1 of 10 | XP_011509231.1 | |||
| GALNT3 | XM_017003770.2 | c.-109+2043T>G | intron_variant | Intron 1 of 10 | XP_016859259.1 | |||
| GALNT3 | XM_047443883.1 | c.-109+1733T>G | intron_variant | Intron 1 of 6 | XP_047299839.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.802 AC: 121939AN: 152002Hom.: 49790 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.802 AC: 122012AN: 152120Hom.: 49811 Cov.: 33 AF XY: 0.801 AC XY: 59540AN XY: 74368
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Feb 18, 2020
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
This variant is associated with the following publications: (PMID: 28453302) -
Computational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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