NM_001422882.1:c.-526-102541G>C

Variant names:

• chr2-153230033-G-C
• rs6741727
• NM_001422882.1:c.-526-102541G>C

Variant summary

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

The NM_001422882.1(GALNT13):​c.-526-102541G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,118 control chromosomes in the GnomAD database, including 3,042 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 0.19 (3042 hom., cov: 32)
• Consequence: GALNT13 NM_001422882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001422882.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT13	NM_001422882.1		c.-526-102541G>C		intron	N/A	NP_001409811.1
	GALNT13	NM_001422883.1		c.-1229-81442G>C		intron	N/A	NP_001409812.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29426 AN: 152000 Hom.: 3039 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.194 AC: 29445 AN: 152118 Hom.: 3042 Cov.: 32 AF XY: 0.188 AC XY: 13952 AN XY: 74362

African (AFR) AF: 0.207 AC: 8609 AN: 41526

American (AMR) AF: 0.154 AC: 2359 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3470

East Asian (EAS) AF: 0.00560 AC: 29 AN: 5174

South Asian (SAS) AF: 0.100 AC: 482 AN: 4822

European-Finnish (FIN) AF: 0.188 AC: 1981 AN: 10564

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.215 AC: 14635 AN: 67970

Other (OTH) AF: 0.190 AC: 401 AN: 2112

Alfa AF: 0.119 Hom.: 193

Bravo AF: 0.192

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.51
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs6741727; hg19: chr2-154086547;