2-153479455-C-T

Position:

• chr2-153479455-C-T

Variant summary

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

The NM_001422879.1(GALNT13):​c.-239+1093C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,130 control chromosomes in the GnomAD database, including 51,531 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 0.81 (51531 hom., cov: 31)
• Consequence: GALNT13 NM_001422879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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]

ENSG00000227400 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT13	NM_001422879.1	c.-239+1093C>T		intron_variant			NP_001409808.1
GALNT13	NM_001422880.1	c.-239+1093C>T		intron_variant			NP_001409809.1
GALNT13	NM_001422881.1	c.-239+70214C>T		intron_variant			NP_001409810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000227400	ENST00000424322.1	n.430-57492G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123566 AN: 152012 Hom.: 51478 Cov.: 31

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.813 AC: 123670 AN: 152130 Hom.: 51531 Cov.: 31 AF XY: 0.803 AC XY: 59732 AN XY: 74360

Gnomad4 AFR AF: 0.925

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.795

Alfa AF: 0.824 Hom.: 6288

Bravo AF: 0.805

Asia WGS AF: 0.530 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.093
DANN	Benign	0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2033764; hg19: chr2-154335968;