2-153516253-T-C

Variant names:

• chr2-153516253-T-C
• rs1221754
• NM_001422879.1:c.-239+37891T>C

Variant summary

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

The NM_001422879.1(GALNT13):​c.-239+37891T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,030 control chromosomes in the GnomAD database, including 6,701 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 0.28 (6701 hom., cov: 32)
• Consequence: GALNT13 NM_001422879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 7 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]

ENSG00000227400 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_001422879.1	c.-239+37891T>C		intron_variant	Intron 2 of 15		NP_001409808.1
GALNT13	NM_001422880.1	c.-239+37891T>C		intron_variant	Intron 2 of 14		NP_001409809.1
GALNT13	NM_001422881.1	c.-239+107012T>C		intron_variant	Intron 1 of 13		NP_001409810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227400	ENST00000424322.1	n.429+76607A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42802 AN: 151912 Hom.: 6686 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.282 AC: 42842 AN: 152030 Hom.: 6701 Cov.: 32 AF XY: 0.286 AC XY: 21222 AN XY: 74302

African (AFR) AF: 0.275 AC: 11408 AN: 41486

American (AMR) AF: 0.427 AC: 6509 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1212 AN: 3466

East Asian (EAS) AF: 0.546 AC: 2812 AN: 5150

South Asian (SAS) AF: 0.387 AC: 1865 AN: 4824

European-Finnish (FIN) AF: 0.181 AC: 1909 AN: 10566

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16066 AN: 67968

Other (OTH) AF: 0.300 AC: 632 AN: 2110

Alfa AF: 0.259 Hom.: 22698

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.44
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1221754; hg19: chr2-154372766;