11-11514333-T-C

Position:

• chr11-11514333-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198516.3(GALNT18):​c.236-65397A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,198 control chromosomes in the GnomAD database, including 2,162 homozygotes. 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: 𝑓 0.16 (2162 hom., cov: 33)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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]

GALNT18 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT18	NM_198516.3	c.236-65397A>G		intron_variant		ENST00000227756.5	NP_940918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.236-65397A>G		intron_variant		1	NM_198516.3	ENSP00000227756.4
GALNT18	ENST00000526064.1	n.401-37881A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24420 AN: 152080 Hom.: 2151 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.164

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.161 AC: 24464 AN: 152198 Hom.: 2162 Cov.: 33 AF XY: 0.157 AC XY: 11707 AN XY: 74422

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0391

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.166

Alfa AF: 0.167 Hom.: 2840

Bravo AF: 0.163

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.59

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: rs7935113; hg19: chr11-11535880;