chr2-153875280-T-C

Variant names:

• chr2-153875280-T-C
• rs1348587
• NM_052917.4:c.-177+2977T>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.-177+2977T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,048 control chromosomes in the GnomAD database, including 7,029 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 0.25 (7029 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 9 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 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.-177+2977T>C		intron	N/A	NP_443149.2	Q8IUC8-1
	GALNT13	NM_001376403.1		c.-177+3104T>C		intron	N/A	NP_001363332.1
	GALNT13	NM_001376404.1		c.-177+2977T>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.-177+2977T>C		intron	N/A	ENSP00000376570.3	Q8IUC8-1
	GALNT13	ENST00000891929.1		c.-177+2977T>C		intron	N/A	ENSP00000561988.1
	GALNT13	ENST00000891932.1		c.-177+3104T>C		intron	N/A	ENSP00000561991.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38635 AN: 151930 Hom.: 7011 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.254 AC: 38693 AN: 152048 Hom.: 7029 Cov.: 32 AF XY: 0.259 AC XY: 19229 AN XY: 74342

African (AFR) AF: 0.405 AC: 16770 AN: 41430

American (AMR) AF: 0.168 AC: 2568 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3468

East Asian (EAS) AF: 0.878 AC: 4543 AN: 5176

South Asian (SAS) AF: 0.401 AC: 1930 AN: 4814

European-Finnish (FIN) AF: 0.131 AC: 1385 AN: 10582

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10152 AN: 67976

Other (OTH) AF: 0.248 AC: 524 AN: 2116

Alfa AF: 0.199 Hom.: 8373

Bravo AF: 0.265

Asia WGS AF: 0.581 AC: 2015 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.86
PhyloP100		-0.50
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: rs1348587; hg19: chr2-154731793;