chr2-154146334-T-C

Variant names:

• chr2-154146334-T-C
• rs16836124
• NM_052917.4:c.311+5829T>C

Variant summary

Our verdict is Benign. Variant got -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

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 (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.311+5829T>C		intron_variant	Intron 4 of 12	ENST00000392825.8	NP_443149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT13	ENST00000392825.8	c.311+5829T>C		intron_variant	Intron 4 of 12	2	NM_052917.4	ENSP00000376570.3
GALNT13	ENST00000409237.5	c.311+5829T>C		intron_variant	Intron 2 of 11	1		ENSP00000387239.1
GALNT13	ENST00000431076.5	n.164+5829T>C		intron_variant	Intron 1 of 8	1		ENSP00000389447.1

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

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0951

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0887

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.0365

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.139

Alfa AF: 0.123 Hom.: 382

Bravo AF: 0.128

Asia WGS AF: 0.160 AC: 559 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.34

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: rs16836124; hg19: chr2-155002847;