2-154370165-T-C

Position:

• chr2-154370165-T-C

Variant summary

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

The NM_052917.4(GALNT13):​c.1157-25826T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,808 control chromosomes in the GnomAD database, including 12,853 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 0.41 (12853 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT13	NM_052917.4	c.1157-25826T>C		intron_variant		ENST00000392825.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT13	ENST00000392825.8	c.1157-25826T>C		intron_variant		2	NM_052917.4	P1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61826 AN: 151688 Hom.: 12852 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.408 AC: 61862 AN: 151808 Hom.: 12853 Cov.: 32 AF XY: 0.404 AC XY: 29943 AN XY: 74198

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.421

Alfa AF: 0.389 Hom.: 14009

Bravo AF: 0.413

Asia WGS AF: 0.408 AC: 1422 AN: 3478

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	0.59

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: rs707040; hg19: chr2-155226677; COSMIC: COSV67236577;