2-154450240-A-T

Variant names:

• chr2-154450240-A-T
• rs707079
• NM_052917.4:c.1531-171A>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.1531-171A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,896 control chromosomes in the GnomAD database, including 31,595 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 0.63 (31595 hom., cov: 32)
• Consequence: GALNT13 NM_052917.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 1 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]

GALNT13-AS1 (HGNC:56700): (GALNT13 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT13	NM_052917.4	c.1531-171A>T		intron_variant	Intron 12 of 12	ENST00000392825.8	NP_443149.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT13	ENST00000392825.8	c.1531-171A>T		intron_variant	Intron 12 of 12	2	NM_052917.4	ENSP00000376570.3

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96055 AN: 151780 Hom.: 31561 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.633 AC: 96139 AN: 151896 Hom.: 31595 Cov.: 32 AF XY: 0.633 AC XY: 46949 AN XY: 74212

African (AFR) AF: 0.804 AC: 33328 AN: 41448

American (AMR) AF: 0.495 AC: 7535 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2181 AN: 3472

East Asian (EAS) AF: 0.870 AC: 4484 AN: 5156

South Asian (SAS) AF: 0.634 AC: 3055 AN: 4822

European-Finnish (FIN) AF: 0.590 AC: 6234 AN: 10562

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37384 AN: 67920

Other (OTH) AF: 0.592 AC: 1240 AN: 2096

Alfa AF: 0.478 Hom.: 1415

Bravo AF: 0.633

Asia WGS AF: 0.712 AC: 2477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.72
DANN	Benign	0.86
PhyloP100		-1.9
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: rs707079; hg19: chr2-155306752;