rs9919560

Positions:

• chr11-11569424-C-A

Variant summary

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

The NM_198516.3(GALNT18):​c.235+51935G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,004 control chromosomes in the GnomAD database, including 4,506 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 0.22 (4506 hom., cov: 32)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

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=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT18	NM_198516.3	c.235+51935G>T		intron_variant		ENST00000227756.5	NP_940918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.235+51935G>T		intron_variant		1	NM_198516.3	ENSP00000227756.4
GALNT18	ENST00000526064.1	n.400+51935G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32977 AN: 151886 Hom.: 4502 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.217 AC: 32978 AN: 152004 Hom.: 4506 Cov.: 32 AF XY: 0.223 AC XY: 16531 AN XY: 74268

Gnomad4 AFR AF: 0.0554

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.240

Alfa AF: 0.280 Hom.: 11769

Bravo AF: 0.195

Asia WGS AF: 0.228 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.4
DANN	Benign	0.82

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: rs9919560; hg19: chr11-11590971;