rs7937567

chr11-11354027-G-Achr11-11354027-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198516.3(GALNT18):c.1093-13023C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,026 control chromosomes in the GnomAD database, including 24,966 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 0.56 (24966 hom., cov: 32)
• Consequence: GALNT18 NM_198516.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT18	NM_198516.3	c.1093-13023C>T		intron_variant		ENST00000227756.5
GALNT18	XM_011520071.4	c.*455C>T		3_prime_UTR_variant	7/7
GALNT18	NM_001363464.2	c.1092+18488C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT18	ENST00000227756.5	c.1093-13023C>T		intron_variant		1	NM_198516.3	P1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85598 AN: 151908 Hom.: 24941 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.563 AC: 85656 AN: 152026 Hom.: 24966 Cov.: 32 AF XY: 0.555 AC XY: 41223 AN XY: 74304

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.563

Alfa AF: 0.556 Hom.: 4777

Bravo AF: 0.557

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.6
Dann	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs7937567; hg19: chr11-11375574;