chr11-11319639-G-A

Variant names:

• chr11-11319639-G-A
• rs1471895
• NM_198516.3:c.1512+7447C>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.1512+7447C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0867 in 152,192 control chromosomes in the GnomAD database, including 737 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 0.087 (737 hom., cov: 33)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.904
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 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.1512+7447C>T		intron	N/A	NP_940918.2
	GALNT18	NM_001363464.2		c.1326+7447C>T		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.1512+7447C>T		intron	N/A	ENSP00000227756.4

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13176 AN: 152074 Hom.: 733 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0603

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0578

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.0867 AC: 13199 AN: 152192 Hom.: 737 Cov.: 33 AF XY: 0.0856 AC XY: 6371 AN XY: 74414

African (AFR) AF: 0.162 AC: 6739 AN: 41498

American (AMR) AF: 0.0602 AC: 921 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3472

East Asian (EAS) AF: 0.0230 AC: 119 AN: 5184

South Asian (SAS) AF: 0.0927 AC: 447 AN: 4822

European-Finnish (FIN) AF: 0.0445 AC: 472 AN: 10604

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0579 AC: 3936 AN: 68000

Other (OTH) AF: 0.0929 AC: 196 AN: 2110

Alfa AF: 0.0685 Hom.: 696

Bravo AF: 0.0903

Asia WGS AF: 0.0620 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.43
PhyloP100		0.90
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: rs1471895; hg19: chr11-11341186;