11-11381685-T-C

Variant names:

• chr11-11381685-T-C
• rs4533032
• NM_198516.3:c.596-2421A>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.596-2421A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,044 control chromosomes in the GnomAD database, including 47,851 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 0.79 (47851 hom., cov: 31)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT18	NM_198516.3	c.596-2421A>G		intron_variant	Intron 3 of 10	ENST00000227756.5	NP_940918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.596-2421A>G		intron_variant	Intron 3 of 10	1	NM_198516.3	ENSP00000227756.4

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119851 AN: 151926 Hom.: 47821 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.789 AC: 119922 AN: 152044 Hom.: 47851 Cov.: 31 AF XY: 0.781 AC XY: 58038 AN XY: 74310

African (AFR) AF: 0.747 AC: 30972 AN: 41464

American (AMR) AF: 0.684 AC: 10449 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3158 AN: 3466

East Asian (EAS) AF: 0.581 AC: 2999 AN: 5158

South Asian (SAS) AF: 0.645 AC: 3110 AN: 4820

European-Finnish (FIN) AF: 0.817 AC: 8627 AN: 10554

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 57968 AN: 67988

Other (OTH) AF: 0.814 AC: 1716 AN: 2108

Alfa AF: 0.830 Hom.: 30927

Bravo AF: 0.778

Asia WGS AF: 0.607 AC: 2109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.9
DANN	Benign	0.78
PhyloP100		0.041
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: rs4533032; hg19: chr11-11403232;