2-154332011-T-G

Variant names:

• chr2-154332011-T-G
• rs707025
• NM_052917.4:c.1156+30422T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 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=-0.82).
• 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 rank	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.1156+30422T>G		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.1156+30422T>G		intron_variant	Intron 9 of 12	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

African (AFR) AF: 0.795 AC: 32998 AN: 41502

American (AMR) AF: 0.625 AC: 9538 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2064 AN: 3472

East Asian (EAS) AF: 0.687 AC: 3529 AN: 5136

South Asian (SAS) AF: 0.652 AC: 3142 AN: 4818

European-Finnish (FIN) AF: 0.590 AC: 6237 AN: 10566

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42865 AN: 67940

Other (OTH) AF: 0.647 AC: 1363 AN: 2108

Alfa AF: 0.644 Hom.: 96130

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
PhyloP100		-0.69
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: rs707025; hg19: chr2-155188523;