2-31024648-G-T

Variant names:

• chr2-31024648-G-T
• rs9679162
• NM_024572.4:c.130-31641C>A

Variant summary

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

The NM_024572.4(GALNT14):​c.130-31641C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,050 control chromosomes in the GnomAD database, including 18,227 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 0.48 (18227 hom., cov: 33)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 35 publications found

Genes affected

GALNT14 (HGNC:22946): (polypeptide N-acetylgalactosaminyltransferase 14) This gene encodes a Golgi protein which is a member of the polypeptide N-acetylgalactosaminyltransferase (ppGalNAc-Ts) protein family. These enzymes catalyze the transfer of N-acetyl-D-galactosamine (GalNAc) to the hydroxyl groups on serines and threonines in target peptides. The encoded protein has been shown to transfer GalNAc to large proteins like mucins. Alterations in this gene may play a role in cancer progression and response to chemotherapy. [provided by RefSeq, Jun 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024572.4. 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
	GALNT14	NM_024572.4	MANE Select	c.130-31641C>A		intron	N/A	NP_078848.2
	GALNT14	NM_001253826.2		c.315-58346C>A		intron	N/A	NP_001240755.1
	GALNT14	NM_001253827.2		c.70-31641C>A		intron	N/A	NP_001240756.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT14	ENST00000349752.10	TSL:1 MANE Select	c.130-31641C>A		intron	N/A	ENSP00000288988.6
	GALNT14	ENST00000464038.5	TSL:1	n.389-31641C>A		intron	N/A
	GALNT14	ENST00000324589.9	TSL:2	c.315-58346C>A		intron	N/A	ENSP00000314500.5

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72698 AN: 151930 Hom.: 18176 Cov.: 33

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.479 AC: 72812 AN: 152050 Hom.: 18227 Cov.: 33 AF XY: 0.475 AC XY: 35291 AN XY: 74342

African (AFR) AF: 0.627 AC: 26000 AN: 41476

American (AMR) AF: 0.537 AC: 8201 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1504 AN: 3472

East Asian (EAS) AF: 0.564 AC: 2916 AN: 5170

South Asian (SAS) AF: 0.378 AC: 1823 AN: 4822

European-Finnish (FIN) AF: 0.341 AC: 3603 AN: 10554

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27268 AN: 67972

Other (OTH) AF: 0.452 AC: 953 AN: 2110

Alfa AF: 0.445 Hom.: 26652

Bravo AF: 0.502

Asia WGS AF: 0.475 AC: 1654 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	1.3
DANN	Benign	0.44
PhyloP100		0.036
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: rs9679162; hg19: chr2-31247514;