rs13407922

chr2-154425285-G-A

Variant summary

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

The NM_052917.4(GALNT13):c.1396-13307G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,082 control chromosomes in the GnomAD database, including 1,501 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 0.13 (1501 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT13	NM_052917.4	c.1396-13307G>A		intron_variant		ENST00000392825.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT13	ENST00000392825.8	c.1396-13307G>A		intron_variant		2	NM_052917.4	P1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20194 AN: 151964 Hom.: 1500 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0880

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.0657

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.133 AC: 20195 AN: 152082 Hom.: 1501 Cov.: 32 AF XY: 0.130 AC XY: 9656 AN XY: 74358

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.0879

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.0655

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.117

Alfa AF: 0.127 Hom.: 215

Bravo AF: 0.132

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.14
Dann	Benign	0.56

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: rs13407922; hg19: chr2-155281797;