chr11-11569424-C-A

Variant names:

• chr11-11569424-C-A
• rs9919560
• NM_198516.3:c.235+51935G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198516.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT18	NM_198516.3	MANE Select	c.235+51935G>T		intron	N/A	NP_940918.2	Q6P9A2-1
	GALNT18	NM_001363464.2		c.235+51935G>T		intron	N/A	NP_001350393.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT18	ENST00000227756.5	TSL:1 MANE Select	c.235+51935G>T		intron	N/A	ENSP00000227756.4	Q6P9A2-1
	GALNT18	ENST00000526064.1	TSL:1	n.400+51935G>T		intron	N/A
	GALNT18	ENST00000958463.1		c.235+51935G>T		intron	N/A	ENSP00000628522.1

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

African (AFR) AF: 0.0554 AC: 2300 AN: 41502

American (AMR) AF: 0.180 AC: 2758 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1065 AN: 3464

East Asian (EAS) AF: 0.118 AC: 608 AN: 5154

South Asian (SAS) AF: 0.382 AC: 1833 AN: 4804

European-Finnish (FIN) AF: 0.345 AC: 3626 AN: 10522

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19945 AN: 67968

Other (OTH) AF: 0.240 AC: 506 AN: 2110

Alfa AF: 0.263 Hom.: 17989

Bravo AF: 0.195

Asia WGS AF: 0.228 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.4
DANN	Benign	0.82
PhyloP100		-0.11
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: rs9919560; hg19: chr11-11590971;