rs1527865

chr2-154357106-C-T

Variant summary

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

The NM_052917.4(GALNT13):c.1157-38885C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 151,734 control chromosomes in the GnomAD database, including 34,872 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 0.67 (34872 hom., cov: 31)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT13	NM_052917.4	c.1157-38885C>T		intron_variant		ENST00000392825.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT13	ENST00000392825.8	c.1157-38885C>T		intron_variant		2	NM_052917.4	P1

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101743 AN: 151620 Hom.: 34849 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.671 AC: 101818 AN: 151734 Hom.: 34872 Cov.: 31 AF XY: 0.675 AC XY: 50059 AN XY: 74146

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.680

Alfa AF: 0.709 Hom.: 76271

Bravo AF: 0.662

Asia WGS AF: 0.673 AC: 2335 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.3
Dann	Benign	0.47

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: rs1527865; hg19: chr2-155213618;