GeneBe

rs2129523

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_198516.3(GALNT18):​c.1093-12378A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

GALNT18
NM_198516.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.427

Publications

3 publications found
Variant links:
Genes affected
GALNT18 (HGNC:30488): (polypeptide N-acetylgalactosaminyltransferase 18) Enables polypeptide N-acetylgalactosaminyltransferase activity. Involved in protein O-linked glycosylation. Predicted to be located in Golgi membrane. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]
CSNK2A3 (HGNC:2458): (casein kinase 2 alpha 3) This gene encodes a protein that is highly similar to the casein kinase II alpha protein. Casein kinase II is a serine/threonine protein kinase complex that phosphorylates numerous substrates including casein. The alpha subunit is the catalytic component of the complex. Mutations in this gene may be associated with a susceptibility to lung cancer. There are contradictory views among published reports of this gene as to whether or not it is a protein-coding gene or a processed pseudogene (PMIDs: 20625391, 20625391 and 10094393). [provided by RefSeq, Feb 2012]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GALNT18NM_198516.3 linkc.1093-12378A>T intron_variant Intron 6 of 10 ENST00000227756.5 NP_940918.2
GALNT18XM_011520071.4 linkc.*1100A>T 3_prime_UTR_variant Exon 7 of 7 XP_011518373.1
GALNT18NM_001363464.2 linkc.1092+19133A>T intron_variant Intron 6 of 9 NP_001350393.1
CSNK2A3NM_001256686.2 linkc.-263A>T upstream_gene_variant ENST00000528848.3 NP_001243615.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GALNT18ENST00000227756.5 linkc.1093-12378A>T intron_variant Intron 6 of 10 1 NM_198516.3 ENSP00000227756.4
CSNK2A3ENST00000528848.3 linkc.-263A>T upstream_gene_variant 6 NM_001256686.2 ENSP00000473553.1
ENSG00000255351ENST00000526867.1 linkn.*75T>A downstream_gene_variant 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
427892
Hom.:
0
Cov.:
3
AF XY:
0.00
AC XY:
0
AN XY:
225634
African (AFR)
AF:
0.00
AC:
0
AN:
12112
American (AMR)
AF:
0.00
AC:
0
AN:
16128
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
13144
East Asian (EAS)
AF:
0.00
AC:
0
AN:
29336
South Asian (SAS)
AF:
0.00
AC:
0
AN:
42050
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
27806
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1874
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
260632
Other (OTH)
AF:
0.00
AC:
0
AN:
24810
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
4.4
DANN
Benign
0.69
PhyloP100
0.43
PromoterAI
-0.0032
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2129523; hg19: chr11-11374929; API