11-11491166-G-T

Variant names:

• chr11-11491166-G-T
• rs1386426
• NM_198516.3:c.236-42230C>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.236-42230C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,120 control chromosomes in the GnomAD database, including 5,511 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 0.25 (5511 hom., cov: 32)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 1 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=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT18	NM_198516.3	c.236-42230C>A		intron_variant	Intron 1 of 10	ENST00000227756.5	NP_940918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.236-42230C>A		intron_variant	Intron 1 of 10	1	NM_198516.3	ENSP00000227756.4
GALNT18	ENST00000526064.1	n.401-14714C>A		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38702 AN: 152002 Hom.: 5499 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.255 AC: 38734 AN: 152120 Hom.: 5511 Cov.: 32 AF XY: 0.254 AC XY: 18901 AN XY: 74380

African (AFR) AF: 0.339 AC: 14060 AN: 41478

American (AMR) AF: 0.391 AC: 5975 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3470

East Asian (EAS) AF: 0.128 AC: 661 AN: 5176

South Asian (SAS) AF: 0.135 AC: 653 AN: 4822

European-Finnish (FIN) AF: 0.195 AC: 2063 AN: 10588

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13856 AN: 67982

Other (OTH) AF: 0.249 AC: 526 AN: 2114

Alfa AF: 0.215 Hom.: 3304

Bravo AF: 0.278

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	3.6
DANN	Benign	0.80
PhyloP100		0.076
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: rs1386426; hg19: chr11-11512713;