chr2-154354666-C-G

Variant names:

• chr2-154354666-C-G
• rs799813
• NM_052917.4:c.1157-41325C>G

Variant summary

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

The NM_001376403.1(GALNT13):​c.1157-41325C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 151,404 control chromosomes in the GnomAD database, including 40,657 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 0.73 (40657 hom., cov: 28)
• Consequence: GALNT13 NM_001376403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001376403.1. 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.1157-41325C>G		intron	N/A	NP_443149.2
	GALNT13	NM_001376403.1		c.1157-41325C>G		intron	N/A	NP_001363332.1
	GALNT13	NM_001376404.1		c.1157-41325C>G		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.1157-41325C>G		intron	N/A	ENSP00000376570.3
	GALNT13	ENST00000409237.5	TSL:1	c.1157-41325C>G		intron	N/A	ENSP00000387239.1
	GALNT13	ENST00000431076.5	TSL:1	n.*977-41325C>G		intron	N/A	ENSP00000389447.1

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110470 AN: 151288 Hom.: 40623 Cov.: 28

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.730 AC: 110550 AN: 151404 Hom.: 40657 Cov.: 28 AF XY: 0.729 AC XY: 53905 AN XY: 73950

African (AFR) AF: 0.768 AC: 31751 AN: 41334

American (AMR) AF: 0.580 AC: 8825 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2431 AN: 3464

East Asian (EAS) AF: 0.580 AC: 2985 AN: 5148

South Asian (SAS) AF: 0.747 AC: 3584 AN: 4798

European-Finnish (FIN) AF: 0.779 AC: 8069 AN: 10354

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50492 AN: 67802

Other (OTH) AF: 0.711 AC: 1491 AN: 2096

Alfa AF: 0.662 Hom.: 1982

Bravo AF: 0.710

Asia WGS AF: 0.671 AC: 2333 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.29
DANN	Benign	0.50
PhyloP100		-1.8
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: rs799813; hg19: chr2-155211178;