2-154332011-T-G

Position:

• chr2-154332011-T-G

Variant summary

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

The NM_052917.4(GALNT13):​c.1156+30422T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 152,000 control chromosomes in the GnomAD database, including 34,993 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 0.67 (34993 hom., cov: 33)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

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]

GALNT13 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.1156+30422T>G		intron_variant		ENST00000392825.8	NP_443149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT13	ENST00000392825.8	c.1156+30422T>G		intron_variant		2	NM_052917.4	ENSP00000376570.3

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102369 AN: 151882 Hom.: 34965 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.674 AC: 102442 AN: 152000 Hom.: 34993 Cov.: 33 AF XY: 0.670 AC XY: 49743 AN XY: 74286

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.647

Alfa AF: 0.629 Hom.: 40203

Bravo AF: 0.686

Asia WGS AF: 0.672 AC: 2328 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.79

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: rs707025; hg19: chr2-155188523;