2-153712244-G-C

Variant names:

• chr2-153712244-G-C
• rs10931753
• NM_001422879.1:c.-238-20525G>C

Variant summary

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

The NM_001422879.1(GALNT13):​c.-238-20525G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,020 control chromosomes in the GnomAD database, including 24,522 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 0.52 (24522 hom., cov: 32)
• Consequence: GALNT13 NM_001422879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_001422879.1	c.-238-20525G>C		intron_variant	Intron 2 of 15		NP_001409808.1
GALNT13	NM_001422880.1	c.-238-20525G>C		intron_variant	Intron 2 of 14		NP_001409809.1
GALNT13	NM_001422881.1	c.-238-20525G>C		intron_variant	Intron 1 of 13		NP_001409810.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78600 AN: 151902 Hom.: 24521 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.517 AC: 78607 AN: 152020 Hom.: 24522 Cov.: 32 AF XY: 0.518 AC XY: 38481 AN XY: 74328

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.545

Alfa AF: 0.607 Hom.: 3748

Bravo AF: 0.492

Asia WGS AF: 0.281 AC: 977 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10931753; hg19: chr2-154568757;