chr11-11514333-T-C

Variant names:

• chr11-11514333-T-C
• rs7935113
• NM_198516.3:c.236-65397A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GALNT18	NM_198516.3	c.236-65397A>G		intron_variant	Intron 1 of 10	ENST00000227756.5	NP_940918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.236-65397A>G		intron_variant	Intron 1 of 10	1	NM_198516.3	ENSP00000227756.4
GALNT18	ENST00000526064.1	n.401-37881A>G		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.196 AC: 8136 AN: 41530

American (AMR) AF: 0.118 AC: 1809 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 681 AN: 3472

East Asian (EAS) AF: 0.0391 AC: 202 AN: 5172

South Asian (SAS) AF: 0.224 AC: 1079 AN: 4822

European-Finnish (FIN) AF: 0.0753 AC: 799 AN: 10608

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11172 AN: 67996

Other (OTH) AF: 0.166 AC: 351 AN: 2112

Alfa AF: 0.167 Hom.: 3598

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
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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: rs7935113; hg19: chr11-11535880;