NM_001422882.1:c.-239+37120A>G

Variant names:

• chr2-153374900-A-G
• rs13397414
• NM_001422882.1:c.-239+37120A>G

Variant summary

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

The NM_001422882.1(GALNT13):​c.-239+37120A>G 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 152,114 control chromosomes in the GnomAD database, including 1,229 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 (1229 hom., cov: 32)
• Consequence: GALNT13 NM_001422882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 8 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_001422882.1	c.-239+37120A>G		intron_variant	Intron 7 of 19		NP_001409811.1
GALNT13	NM_001422883.1	c.-613+41573A>G		intron_variant	Intron 5 of 16		NP_001409812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18020 AN: 151996 Hom.: 1228 Cov.: 32

Gnomad AFR AF: 0.0839

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.118 AC: 18016 AN: 152114 Hom.: 1229 Cov.: 32 AF XY: 0.121 AC XY: 8998 AN XY: 74364

African (AFR) AF: 0.0839 AC: 3481 AN: 41512

American (AMR) AF: 0.0739 AC: 1129 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3468

East Asian (EAS) AF: 0.0420 AC: 217 AN: 5168

South Asian (SAS) AF: 0.166 AC: 800 AN: 4824

European-Finnish (FIN) AF: 0.197 AC: 2085 AN: 10574

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.138 AC: 9373 AN: 67980

Other (OTH) AF: 0.107 AC: 226 AN: 2114

Alfa AF: 0.139 Hom.: 1009

Bravo AF: 0.106

Asia WGS AF: 0.112 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.4
DANN	Benign	0.72
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs13397414; hg19: chr2-154231414;