chr2-154043812-G-T

Variant names:

• chr2-154043812-G-T
• rs1863086
• NM_052917.4:c.143-96525G>T

Variant summary

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

The NM_052917.4(GALNT13):​c.143-96525G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,918 control chromosomes in the GnomAD database, including 21,755 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 (21755 hom., cov: 31)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 6 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052917.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT13	NM_052917.4	MANE Select	c.143-96525G>T		intron	N/A	NP_443149.2	Q8IUC8-1
	GALNT13	NM_001376403.1		c.143-96525G>T		intron	N/A	NP_001363332.1
	GALNT13	NM_001376404.1		c.143-96525G>T		intron	N/A	NP_001363333.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT13	ENST00000392825.8	TSL:2 MANE Select	c.143-96525G>T		intron	N/A	ENSP00000376570.3	Q8IUC8-1
	GALNT13	ENST00000409237.5	TSL:1	c.143-96525G>T		intron	N/A	ENSP00000387239.1	Q8IUC8-3
	GALNT13	ENST00000891929.1		c.187+30703G>T		intron	N/A	ENSP00000561988.1

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78983 AN: 151800 Hom.: 21727 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.520 AC: 79054 AN: 151918 Hom.: 21755 Cov.: 31 AF XY: 0.525 AC XY: 38951 AN XY: 74244

African (AFR) AF: 0.620 AC: 25703 AN: 41440

American (AMR) AF: 0.396 AC: 6043 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3468

East Asian (EAS) AF: 0.955 AC: 4898 AN: 5130

South Asian (SAS) AF: 0.641 AC: 3090 AN: 4818

European-Finnish (FIN) AF: 0.444 AC: 4688 AN: 10550

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31038 AN: 67948

Other (OTH) AF: 0.558 AC: 1176 AN: 2108

Alfa AF: 0.468 Hom.: 28124

Bravo AF: 0.523

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.026
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: rs1863086; hg19: chr2-154900325;