NM_024572.4:c.129+49471A>G

Variant names:

• chr2-31088487-T-C
• rs10490518
• NM_024572.4:c.129+49471A>G

Variant summary

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

The NM_024572.4(GALNT14):​c.129+49471A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,938 control chromosomes in the GnomAD database, including 15,452 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 0.44 (15452 hom., cov: 31)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 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.129+49471A>G		intron	N/A	NP_078848.2
	GALNT14	NM_001253826.2		c.314+26256A>G		intron	N/A	NP_001240755.1
	GALNT14	NM_001253827.2		c.69+26256A>G		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.129+49471A>G		intron	N/A	ENSP00000288988.6
	GALNT14	ENST00000464038.5	TSL:1	n.388+58435A>G		intron	N/A
	GALNT14	ENST00000324589.9	TSL:2	c.314+26256A>G		intron	N/A	ENSP00000314500.5

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67483 AN: 151820 Hom.: 15444 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.444 AC: 67526 AN: 151938 Hom.: 15452 Cov.: 31 AF XY: 0.441 AC XY: 32789 AN XY: 74274

African (AFR) AF: 0.459 AC: 18999 AN: 41428

American (AMR) AF: 0.457 AC: 6962 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1205 AN: 3466

East Asian (EAS) AF: 0.161 AC: 829 AN: 5150

South Asian (SAS) AF: 0.315 AC: 1519 AN: 4816

European-Finnish (FIN) AF: 0.502 AC: 5304 AN: 10564

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31306 AN: 67950

Other (OTH) AF: 0.412 AC: 869 AN: 2108

Alfa AF: 0.335 Hom.: 908

Bravo AF: 0.439

Asia WGS AF: 0.273 AC: 949 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.33
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs10490518; hg19: chr2-31311353;