chr11-11353382-T-G

Variant names:

• chr11-11353382-T-G
• rs2129523
• NM_198516.3:c.1093-12378A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_198516.3(GALNT18):​c.1093-12378A>C 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)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427
• Publications: 3 publications found

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]

ENSG00000255351 (HGNC:):

ACMG classification

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=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198516.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT18	NM_198516.3	MANE Select	c.1093-12378A>C		intron	N/A	NP_940918.2
	GALNT18	NM_001363464.2		c.1092+19133A>C		intron	N/A	NP_001350393.1
	CSNK2A3	NM_001256686.2	MANE Select	c.-263A>C		upstream_gene	N/A	NP_001243615.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT18	ENST00000227756.5	TSL:1 MANE Select	c.1093-12378A>C		intron	N/A	ENSP00000227756.4
	CSNK2A3	ENST00000528848.3	TSL:6 MANE Select	c.-263A>C		upstream_gene	N/A	ENSP00000473553.1
	ENSG00000255351	ENST00000526867.1	TSL:3	n.*75T>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 3

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.6
DANN	Benign	0.62
PhyloP100		0.43
PromoterAI		0.014	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

Other links and lift over

dbSNP: rs2129523; hg19: chr11-11374929;