rs1468995

chr2-154160912-C-Achr2-154160912-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.311+20407C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,204 control chromosomes in the GnomAD database, including 3,330 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 0.18 (3330 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT13	NM_052917.4	c.311+20407C>A		intron_variant		ENST00000392825.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT13	ENST00000392825.8	c.311+20407C>A		intron_variant		2	NM_052917.4	P1
GALNT13	ENST00000409237.5	c.311+20407C>A		intron_variant		1
GALNT13	ENST00000431076.5	c.165+20407C>A		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27781 AN: 152086 Hom.: 3329 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.183 AC: 27781 AN: 152204 Hom.: 3330 Cov.: 32 AF XY: 0.179 AC XY: 13344 AN XY: 74402

Gnomad4 AFR AF: 0.0478

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.153

Alfa AF: 0.156 Hom.: 451

Bravo AF: 0.168

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.1
Dann	Benign	0.67

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: rs1468995; hg19: chr2-155017425;