11-11305011-C-T

Variant summary

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

The NM_198516.3(GALNT18):c.1513-11818G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,150 control chromosomes in the GnomAD database, including 1,646 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 (1646 hom., cov: 33)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT18	NM_198516.3	c.1513-11818G>A		intron_variant		ENST00000227756.5
GALNT18	NM_001363464.2	c.1327-11818G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT18	ENST00000227756.5	c.1513-11818G>A		intron_variant		1	NM_198516.3	P1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19404 AN: 152032 Hom.: 1647 Cov.: 33

Gnomad AFR AF: 0.0303

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0349

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.128 AC: 19402 AN: 152150 Hom.: 1646 Cov.: 33 AF XY: 0.128 AC XY: 9523 AN XY: 74378

Gnomad4 AFR AF: 0.0302

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0350

Gnomad4 SAS AF: 0.0764

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.142

Alfa AF: 0.153 Hom.: 926

Bravo AF: 0.126

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.0010
Dann	Benign	0.57

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: rs12797711; hg19: chr11-11326558;