rs7131111

chr11-11368035-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.1092+4480G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0316 in 152,216 control chromosomes in the GnomAD database, including 115 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 0.032 (115 hom., cov: 33)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT18	NM_198516.3	c.1092+4480G>A		intron_variant		ENST00000227756.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT18	ENST00000227756.5	c.1092+4480G>A		intron_variant		1	NM_198516.3	P1

Frequencies

GnomAD3 genomes AF: 0.0316 AC: 4808 AN: 152098 Hom.: 114 Cov.: 33

Gnomad AFR AF: 0.00973

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0468

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.0639

Gnomad SAS AF: 0.0763

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0356

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0316 AC: 4806 AN: 152216 Hom.: 115 Cov.: 33 AF XY: 0.0326 AC XY: 2427 AN XY: 74408

Gnomad4 AFR AF: 0.00975

Gnomad4 AMR AF: 0.0468

Gnomad4 ASJ AF: 0.0683

Gnomad4 EAS AF: 0.0637

Gnomad4 SAS AF: 0.0767

Gnomad4 FIN AF: 0.0106

Gnomad4 NFE AF: 0.0356

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0346 Hom.: 15

Bravo AF: 0.0328

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.33
Dann	Benign	0.40

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: rs7131111; hg19: chr11-11389582;