rs16836124

Variant names:

• chr2-154146334-T-C
• rs16836124
• NM_052917.4:c.311+5829T>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.311+5829T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 151,946 control chromosomes in the GnomAD database, including 1,302 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 0.12 (1302 hom., cov: 30)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052917.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT13	NM_052917.4	MANE Select	c.311+5829T>C		intron	N/A	NP_443149.2	Q8IUC8-1
	GALNT13	NM_001376403.1		c.311+5829T>C		intron	N/A	NP_001363332.1
	GALNT13	NM_001376404.1		c.311+5829T>C		intron	N/A	NP_001363333.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT13	ENST00000392825.8	TSL:2 MANE Select	c.311+5829T>C		intron	N/A	ENSP00000376570.3	Q8IUC8-1
	GALNT13	ENST00000409237.5	TSL:1	c.311+5829T>C		intron	N/A	ENSP00000387239.1	Q8IUC8-3
	GALNT13	ENST00000431076.5	TSL:1	n.164+5829T>C		intron	N/A	ENSP00000389447.1	H7BZG2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18882 AN: 151828 Hom.: 1301 Cov.: 30

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.0953

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0885

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.0365

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.124 AC: 18893 AN: 151946 Hom.: 1302 Cov.: 30 AF XY: 0.121 AC XY: 9023 AN XY: 74278

African (AFR) AF: 0.137 AC: 5691 AN: 41488

American (AMR) AF: 0.0951 AC: 1449 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3466

East Asian (EAS) AF: 0.0887 AC: 459 AN: 5172

South Asian (SAS) AF: 0.212 AC: 1019 AN: 4804

European-Finnish (FIN) AF: 0.0365 AC: 387 AN: 10598

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8804 AN: 67864

Other (OTH) AF: 0.139 AC: 293 AN: 2110

Alfa AF: 0.128 Hom.: 1035

Bravo AF: 0.128

Asia WGS AF: 0.160 AC: 559 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.34
PhyloP100		1.4
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: rs16836124; hg19: chr2-155002847;