rs1471895

Positions:

• chr11-11319639-G-A
• chr11-11319639-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT18	NM_198516.3	c.1512+7447C>T		intron_variant		ENST00000227756.5	NP_940918.2
GALNT18	NM_001363464.2	c.1326+7447C>T		intron_variant			NP_001350393.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT18	ENST00000227756.5	c.1512+7447C>T		intron_variant		1	NM_198516.3	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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0602

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.0230

Gnomad4 SAS AF: 0.0927

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.0929

Alfa AF: 0.0653 Hom.: 417

Bravo AF: 0.0903

Asia WGS AF: 0.0620 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.8
DANN	Benign	0.43

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: rs1471895; hg19: chr11-11341186;