rs17439526

Variant names:

• chr2-153974821-T-C
• rs17439526
• NM_052917.4:c.142+30182T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.142+30182T>C		intron_variant	Intron 3 of 12	ENST00000392825.8	NP_443149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT13	ENST00000392825.8	c.142+30182T>C		intron_variant	Intron 3 of 12	2	NM_052917.4	ENSP00000376570.3
GALNT13	ENST00000409237.5	c.142+30182T>C		intron_variant	Intron 1 of 11	1		ENSP00000387239.1

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

African (AFR) AF: 0.150 AC: 6210 AN: 41508

American (AMR) AF: 0.218 AC: 3332 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1094 AN: 3468

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5180

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4822

European-Finnish (FIN) AF: 0.287 AC: 3025 AN: 10550

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20591 AN: 67782

Other (OTH) AF: 0.209 AC: 442 AN: 2110

Alfa AF: 0.263 Hom.: 922

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
PhyloP100		0.074
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17439526; hg19: chr2-154831334;