11-11607784-C-T

Variant names:

• chr11-11607784-C-T
• rs11021955
• NM_198516.3:c.235+13575G>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.235+13575G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0997 in 152,194 control chromosomes in the GnomAD database, including 836 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 0.10 (836 hom., cov: 32)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 0 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT18	NM_198516.3	MANE Select	c.235+13575G>A		intron	N/A	NP_940918.2
	GALNT18	NM_001363464.2		c.235+13575G>A		intron	N/A	NP_001350393.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT18	ENST00000227756.5	TSL:1 MANE Select	c.235+13575G>A		intron	N/A	ENSP00000227756.4
	GALNT18	ENST00000526064.1	TSL:1	n.400+13575G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0997 AC: 15162 AN: 152076 Hom.: 834 Cov.: 32

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.0997 AC: 15171 AN: 152194 Hom.: 836 Cov.: 32 AF XY: 0.0982 AC XY: 7307 AN XY: 74398

African (AFR) AF: 0.0553 AC: 2294 AN: 41520

American (AMR) AF: 0.105 AC: 1609 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3470

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5184

South Asian (SAS) AF: 0.0871 AC: 419 AN: 4812

European-Finnish (FIN) AF: 0.112 AC: 1185 AN: 10592

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8882 AN: 68016

Other (OTH) AF: 0.118 AC: 249 AN: 2116

Alfa AF: 0.115 Hom.: 1903

Bravo AF: 0.0963

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.0
DANN	Benign	0.66
PhyloP100		0.17
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: rs11021955; hg19: chr11-11629331;