rs17439526

Positions:

• chr2-153974821-T-C

Variant summary

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

The NM_052917.4(GALNT13):​c.142+30182T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,888 control chromosomes in the GnomAD database, including 4,842 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 0.24 (4842 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT13	NM_052917.4	c.142+30182T>C		intron_variant		ENST00000392825.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT13	ENST00000392825.8	c.142+30182T>C		intron_variant		2	NM_052917.4	P1
GALNT13	ENST00000409237.5	c.142+30182T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36165 AN: 151770 Hom.: 4837 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.238 AC: 36179 AN: 151888 Hom.: 4842 Cov.: 32 AF XY: 0.234 AC XY: 17354 AN XY: 74240

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.209

Alfa AF: 0.268 Hom.: 910

Bravo AF: 0.227

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.77

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: rs17439526; hg19: chr2-154831334;