2-153074663-G-C

Variant names:

• chr2-153074663-G-C
• rs1367374
• NM_001422882.1:c.-868-3677G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001422882.1(GALNT13):​c.-868-3677G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,058 control chromosomes in the GnomAD database, including 3,058 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 (3058 hom., cov: 32)
• Consequence: GALNT13 NM_001422882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_001422882.1	c.-868-3677G>C		intron_variant	Intron 1 of 19		NP_001409811.1
GALNT13	NM_001422883.1	c.-1344-3677G>C		intron_variant	Intron 1 of 16		NP_001409812.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28681 AN: 151942 Hom.: 3060 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.189 AC: 28695 AN: 152058 Hom.: 3058 Cov.: 32 AF XY: 0.187 AC XY: 13919 AN XY: 74326

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.172

Alfa AF: 0.0843 Hom.: 100

Bravo AF: 0.194

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1367374; hg19: chr2-153931177;