rs12278731

Variant names:

• chr11-11445066-C-T
• rs12278731
• NM_198516.3:c.428+3678G>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.428+3678G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,144 control chromosomes in the GnomAD database, including 18,785 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 0.47 (18785 hom., cov: 33)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT18	NM_198516.3	c.428+3678G>A		intron_variant	Intron 2 of 10	ENST00000227756.5	NP_940918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.428+3678G>A		intron_variant	Intron 2 of 10	1	NM_198516.3	ENSP00000227756.4

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72059 AN: 152026 Hom.: 18784 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.474 AC: 72062 AN: 152144 Hom.: 18785 Cov.: 33 AF XY: 0.473 AC XY: 35177 AN XY: 74364

African (AFR) AF: 0.241 AC: 10007 AN: 41518

American (AMR) AF: 0.499 AC: 7637 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2202 AN: 3472

East Asian (EAS) AF: 0.369 AC: 1904 AN: 5164

South Asian (SAS) AF: 0.440 AC: 2123 AN: 4820

European-Finnish (FIN) AF: 0.582 AC: 6154 AN: 10576

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 40058 AN: 67976

Other (OTH) AF: 0.507 AC: 1072 AN: 2114

Alfa AF: 0.557 Hom.: 41476

Bravo AF: 0.460

Asia WGS AF: 0.388 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.085
DANN	Benign	0.60
PhyloP100		-1.2
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: rs12278731; hg19: chr11-11466613;