rs7937567

Variant names:

• chr11-11354027-G-A
• rs7937567
• NM_198516.3:c.1093-13023C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-11354027-G-A
• chr11-11354027-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 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.1093-13023C>T		intron	N/A	NP_940918.2	Q6P9A2-1
	GALNT18	NM_001363464.2		c.1092+18488C>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.1093-13023C>T		intron	N/A	ENSP00000227756.4	Q6P9A2-1
	GALNT18	ENST00000958463.1		c.1093-13023C>T		intron	N/A	ENSP00000628522.1
	GALNT18	ENST00000878654.1		c.1093-13023C>T		intron	N/A	ENSP00000548713.1

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

African (AFR) AF: 0.608 AC: 25192 AN: 41458

American (AMR) AF: 0.453 AC: 6930 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2030 AN: 3466

East Asian (EAS) AF: 0.125 AC: 648 AN: 5164

South Asian (SAS) AF: 0.411 AC: 1975 AN: 4808

European-Finnish (FIN) AF: 0.569 AC: 6009 AN: 10564

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.602 AC: 40915 AN: 67964

Other (OTH) AF: 0.563 AC: 1188 AN: 2110

Alfa AF: 0.581 Hom.: 36131

Bravo AF: 0.557

Asia WGS AF: 0.330 AC: 1149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.67
PhyloP100		0.067
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: rs7937567; hg19: chr11-11375574;