2-154370165-T-C

Variant names:

• chr2-154370165-T-C
• rs707040
• NM_052917.4:c.1157-25826T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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]

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 (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.1157-25826T>C		intron_variant	Intron 9 of 12	ENST00000392825.8	NP_443149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT13	ENST00000392825.8	c.1157-25826T>C		intron_variant	Intron 9 of 12	2	NM_052917.4	ENSP00000376570.3

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

African (AFR) AF: 0.488 AC: 20188 AN: 41396

American (AMR) AF: 0.342 AC: 5196 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1959 AN: 5152

South Asian (SAS) AF: 0.448 AC: 2156 AN: 4812

European-Finnish (FIN) AF: 0.329 AC: 3481 AN: 10572

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.377 AC: 25625 AN: 67894

Other (OTH) AF: 0.421 AC: 889 AN: 2112

Alfa AF: 0.395 Hom.: 23888

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
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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