rs16834756

chr2-153888496-A-G

Variant summary

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

The NM_052917.4(GALNT13):c.-176-12440A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0535 in 152,078 control chromosomes in the GnomAD database, including 310 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 0.053 (310 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.925

Genes affected

GALNT13 (HGNC:23242): (polypeptide N-acetylgalactosaminyltransferase 13) The GALNT13 protein is a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAcT; EC 2.4.1.41) family, which initiate O-linked glycosylation of mucins (see MUC3A, MIM 158371) by the initial transfer of N-acetylgalactosamine (GalNAc) with an alpha-linkage to a serine or threonine residue.[supplied by OMIM, Apr 2004]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT13	NM_052917.4	c.-176-12440A>G		intron_variant		ENST00000392825.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT13	ENST00000392825.8	c.-176-12440A>G		intron_variant		2	NM_052917.4	P1
GALNT13	ENST00000434213.1	c.-228-12440A>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0534 AC: 8122 AN: 151960 Hom.: 310 Cov.: 32

Gnomad AFR AF: 0.0945

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0332

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0101

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0557

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

GnomAD4 genome AF: 0.0535 AC: 8136 AN: 152078 Hom.: 310 Cov.: 32 AF XY: 0.0524 AC XY: 3893 AN XY: 74356

Gnomad4 AFR AF: 0.0946

Gnomad4 AMR AF: 0.0336

Gnomad4 ASJ AF: 0.0332

Gnomad4 EAS AF: 0.00483

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0101

Gnomad4 NFE AF: 0.0398

Gnomad4 OTH AF: 0.0556

Alfa AF: 0.0472 Hom.: 95

Bravo AF: 0.0559

Asia WGS AF: 0.0620 AC: 217 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.75
Dann	Benign	0.57

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: rs16834756; hg19: chr2-154745009;