2-154438146-T-C

Variant names:

• chr2-154438146-T-C
• rs1405934
• NM_052917.4:c.1396-446T>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.1396-446T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,124 control chromosomes in the GnomAD database, including 1,180 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 0.12 (1180 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• 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]

GALNT13-AS1 (HGNC:56700): (GALNT13 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.1396-446T>C		intron_variant	Intron 11 of 12	ENST00000392825.8	NP_443149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT13	ENST00000392825.8	c.1396-446T>C		intron_variant	Intron 11 of 12	2	NM_052917.4	ENSP00000376570.3

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17870 AN: 152004 Hom.: 1174 Cov.: 32

Gnomad AFR AF: 0.0931

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.0998

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.118 AC: 17893 AN: 152124 Hom.: 1180 Cov.: 32 AF XY: 0.118 AC XY: 8757 AN XY: 74362

African (AFR) AF: 0.0934 AC: 3880 AN: 41520

American (AMR) AF: 0.0996 AC: 1524 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 671 AN: 3464

East Asian (EAS) AF: 0.236 AC: 1215 AN: 5152

South Asian (SAS) AF: 0.125 AC: 601 AN: 4818

European-Finnish (FIN) AF: 0.0940 AC: 995 AN: 10582

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8495 AN: 67976

Other (OTH) AF: 0.138 AC: 291 AN: 2110

Alfa AF: 0.0978 Hom.: 352

Bravo AF: 0.118

Asia WGS AF: 0.163 AC: 566 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		0.057
PromoterAI		0.0050	Neutral
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: rs1405934; hg19: chr2-155294658;