2-154097177-C-T

Variant names:

• chr2-154097177-C-T
• rs10175397
• NM_052917.4:c.143-43160C>T

Variant summary

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

The NM_052917.4(GALNT13):​c.143-43160C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 151,858 control chromosomes in the GnomAD database, including 43,738 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 0.76 (43738 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.143-43160C>T		intron_variant	Intron 3 of 12	ENST00000392825.8	NP_443149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT13	ENST00000392825.8	c.143-43160C>T		intron_variant	Intron 3 of 12	2	NM_052917.4	ENSP00000376570.3
GALNT13	ENST00000409237.5	c.143-43160C>T		intron_variant	Intron 1 of 11	1		ENSP00000387239.1

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114667 AN: 151738 Hom.: 43686 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.756 AC: 114776 AN: 151858 Hom.: 43738 Cov.: 32 AF XY: 0.756 AC XY: 56119 AN XY: 74202

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.768

Alfa AF: 0.739 Hom.: 7046

Bravo AF: 0.747

Asia WGS AF: 0.855 AC: 2969 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10175397; hg19: chr2-154953690;