11-11353382-T-A

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

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

Verdict is Likely_benign. Variant got -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
GALNT18	NM_198516.3	c.1093-12378A>T		intron_variant	Intron 6 of 10	ENST00000227756.5	NP_940918.2
GALNT18	XM_011520071.4	c.*1100A>T		3_prime_UTR_variant	Exon 7 of 7		XP_011518373.1
GALNT18	NM_001363464.2	c.1092+19133A>T		intron_variant	Intron 6 of 9		NP_001350393.1
CSNK2A3	NM_001256686.2	c.-263A>T		upstream_gene_variant		ENST00000528848.3	NP_001243615.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.1093-12378A>T		intron_variant	Intron 6 of 10	1	NM_198516.3	ENSP00000227756.4
CSNK2A3	ENST00000528848.3	c.-263A>T		upstream_gene_variant		6	NM_001256686.2	ENSP00000473553.1
ENSG00000255351	ENST00000526867.1	n.*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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

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

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

LitVar

Other links and lift over

dbSNP: rs2129523; hg19: chr11-11374929;