2-154385687-A-T

Variant names:

• chr2-154385687-A-T
• rs12478741
• NM_052917.4:c.1157-10304A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052917.4(GALNT13):​c.1157-10304A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0557 in 152,082 control chromosomes in the GnomAD database, including 268 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 0.056 (268 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.1157-10304A>T		intron_variant	Intron 9 of 12	ENST00000392825.8	NP_443149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT13	ENST00000392825.8	c.1157-10304A>T		intron_variant	Intron 9 of 12	2	NM_052917.4	ENSP00000376570.3

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8464 AN: 151964 Hom.: 269 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0652

Gnomad ASJ AF: 0.0780

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0642

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0557 AC: 8465 AN: 152082 Hom.: 268 Cov.: 32 AF XY: 0.0561 AC XY: 4170 AN XY: 74360

African (AFR) AF: 0.0275 AC: 1144 AN: 41530

American (AMR) AF: 0.0652 AC: 995 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0780 AC: 270 AN: 3462

East Asian (EAS) AF: 0.102 AC: 529 AN: 5166

South Asian (SAS) AF: 0.0684 AC: 330 AN: 4822

European-Finnish (FIN) AF: 0.0539 AC: 572 AN: 10618

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0642 AC: 4360 AN: 67912

Other (OTH) AF: 0.0777 AC: 164 AN: 2110

Alfa AF: 0.0279 Hom.: 15

Bravo AF: 0.0546

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.9
DANN	Benign	0.73
PhyloP100		0.16
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: rs12478741; hg19: chr2-155242199;