1-230067417-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_004481.5(GALNT2):c.126+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000317 in 1,135,896 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00018 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0000091 ( 0 hom. )
Consequence
GALNT2
NM_004481.5 intron
NM_004481.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.195
Genes affected
GALNT2 (HGNC:4124): (polypeptide N-acetylgalactosaminyltransferase 2) This gene encodes a member of the glycosyltransferase 2 protein family. Members of this family initiate mucin-type O-glycoslation of peptides in the Golgi apparatus. The encoded protein may be involved in O-linked glycosylation of the immunoglobulin A1 hinge region. This gene may influence triglyceride levels, and may be involved Type 2 diabetes, as well as several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 1-230067417-C-T is Benign according to our data. Variant chr1-230067417-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3627717.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000179 (27/150962) while in subpopulation AMR AF= 0.000659 (10/15184). AF 95% confidence interval is 0.000357. There are 1 homozygotes in gnomad4. There are 15 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALNT2 | NM_004481.5 | c.126+11C>T | intron_variant | Intron 1 of 15 | ENST00000366672.5 | NP_004472.1 | ||
GALNT2 | NM_001291866.2 | c.12+9339C>T | intron_variant | Intron 1 of 15 | NP_001278795.1 | |||
GALNT2 | NR_120373.2 | n.169+11C>T | intron_variant | Intron 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GALNT2 | ENST00000366672.5 | c.126+11C>T | intron_variant | Intron 1 of 15 | 1 | NM_004481.5 | ENSP00000355632.4 | |||
GALNT2 | ENST00000488903.1 | n.148+11C>T | intron_variant | Intron 1 of 1 | 2 | |||||
GALNT2 | ENST00000494106.1 | n.89+9339C>T | intron_variant | Intron 1 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000179 AC: 27AN: 150854Hom.: 1 Cov.: 32
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GnomAD4 exome AF: 0.00000914 AC: 9AN: 984934Hom.: 0 Cov.: 15 AF XY: 0.00000634 AC XY: 3AN XY: 473206
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GnomAD4 genome AF: 0.000179 AC: 27AN: 150962Hom.: 1 Cov.: 32 AF XY: 0.000203 AC XY: 15AN XY: 73776
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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
Dec 03, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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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