rs16909324

Variant names:

• chr11-11285139-C-T
• rs16909324
• NM_198516.3:c.1677+7890G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198516.3(GALNT18):​c.1677+7890G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,790 control chromosomes in the GnomAD database, including 1,390 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 0.13 (1390 hom., cov: 31)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT18	NM_198516.3	c.1677+7890G>A		intron_variant	Intron 10 of 10	ENST00000227756.5	NP_940918.2
GALNT18	NM_001363464.2	c.1491+7890G>A		intron_variant	Intron 9 of 9		NP_001350393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.1677+7890G>A		intron_variant	Intron 10 of 10	1	NM_198516.3	ENSP00000227756.4

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19151 AN: 151672 Hom.: 1383 Cov.: 31

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.126 AC: 19177 AN: 151790 Hom.: 1390 Cov.: 31 AF XY: 0.129 AC XY: 9574 AN XY: 74188

African (AFR) AF: 0.0832 AC: 3441 AN: 41344

American (AMR) AF: 0.180 AC: 2741 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 448 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1144 AN: 5146

South Asian (SAS) AF: 0.110 AC: 527 AN: 4802

European-Finnish (FIN) AF: 0.177 AC: 1862 AN: 10518

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8584 AN: 67930

Other (OTH) AF: 0.121 AC: 256 AN: 2114

Alfa AF: 0.124 Hom.: 159

Bravo AF: 0.124

Asia WGS AF: 0.176 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.039
DANN	Benign	0.66
PhyloP100		-2.2
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: rs16909324; hg19: chr11-11306686;