chr2-154214054-A-T

Variant names:

• chr2-154214054-A-T
• rs958672
• NM_052917.4:c.312-27976A>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.312-27976A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,116 control chromosomes in the GnomAD database, including 50,758 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 0.81 (50758 hom., cov: 31)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT13	NM_052917.4	MANE Select	c.312-27976A>T		intron	N/A	NP_443149.2
	GALNT13	NM_001376403.1		c.312-27976A>T		intron	N/A	NP_001363332.1
	GALNT13	NM_001376404.1		c.312-27976A>T		intron	N/A	NP_001363333.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT13	ENST00000392825.8	TSL:2 MANE Select	c.312-27976A>T		intron	N/A	ENSP00000376570.3
	GALNT13	ENST00000409237.5	TSL:1	c.312-27976A>T		intron	N/A	ENSP00000387239.1
	GALNT13	ENST00000431076.5	TSL:1	n.165-21992A>T		intron	N/A	ENSP00000389447.1

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123003 AN: 151998 Hom.: 50712 Cov.: 31

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.809 AC: 123101 AN: 152116 Hom.: 50758 Cov.: 31 AF XY: 0.806 AC XY: 59938 AN XY: 74348

African (AFR) AF: 0.949 AC: 39422 AN: 41524

American (AMR) AF: 0.684 AC: 10452 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2998 AN: 3472

East Asian (EAS) AF: 0.977 AC: 5044 AN: 5162

South Asian (SAS) AF: 0.828 AC: 3993 AN: 4822

European-Finnish (FIN) AF: 0.713 AC: 7526 AN: 10560

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50884 AN: 67984

Other (OTH) AF: 0.829 AC: 1751 AN: 2112

Alfa AF: 0.767 Hom.: 24980

Bravo AF: 0.813

Asia WGS AF: 0.875 AC: 3044 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.60
PhyloP100		0.37
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: rs958672; hg19: chr2-155070567;