11-11448205-G-T

Variant names:

• chr11-11448205-G-T
• rs9988868
• NM_198516.3:c.428+539C>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.428+539C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,806 control chromosomes in the GnomAD database, including 11,336 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 0.37 (11336 hom., cov: 31)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT18	NM_198516.3	c.428+539C>A		intron_variant	Intron 2 of 10	ENST00000227756.5	NP_940918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.428+539C>A		intron_variant	Intron 2 of 10	1	NM_198516.3	ENSP00000227756.4

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56567 AN: 151686 Hom.: 11334 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.373 AC: 56566 AN: 151806 Hom.: 11336 Cov.: 31 AF XY: 0.374 AC XY: 27747 AN XY: 74192

African (AFR) AF: 0.215 AC: 8912 AN: 41366

American (AMR) AF: 0.301 AC: 4593 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1725 AN: 3466

East Asian (EAS) AF: 0.334 AC: 1713 AN: 5132

South Asian (SAS) AF: 0.425 AC: 2039 AN: 4798

European-Finnish (FIN) AF: 0.473 AC: 4981 AN: 10532

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31108 AN: 67946

Other (OTH) AF: 0.391 AC: 825 AN: 2108

Alfa AF: 0.429 Hom.: 61262

Bravo AF: 0.349

Asia WGS AF: 0.349 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.54
PhyloP100		0.078
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: rs9988868; hg19: chr11-11469752;