2-31091689-T-C

Variant names:

• chr2-31091689-T-C
• rs1000916
• NM_024572.4:c.129+46269A>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+46269A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0617 in 152,292 control chromosomes in the GnomAD database, including 436 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 0.062 (436 hom., cov: 32)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.129+46269A>G		intron_variant	Intron 1 of 14	ENST00000349752.10	NP_078848.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT14	ENST00000349752.10	c.129+46269A>G		intron_variant	Intron 1 of 14	1	NM_024572.4	ENSP00000288988.6

Frequencies

GnomAD3 genomes AF: 0.0616 AC: 9381 AN: 152174 Hom.: 432 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0374

Gnomad ASJ AF: 0.0680

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.0807

Gnomad FIN AF: 0.00997

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0352

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0617 AC: 9396 AN: 152292 Hom.: 436 Cov.: 32 AF XY: 0.0599 AC XY: 4463 AN XY: 74482

Gnomad4 AFR AF: 0.128 AC: 0.127528 AN: 0.127528

Gnomad4 AMR AF: 0.0373 AC: 0.0372549 AN: 0.0372549

Gnomad4 ASJ AF: 0.0680 AC: 0.0680115 AN: 0.0680115

Gnomad4 EAS AF: 0.0476 AC: 0.0476099 AN: 0.0476099

Gnomad4 SAS AF: 0.0801 AC: 0.0801162 AN: 0.0801162

Gnomad4 FIN AF: 0.00997 AC: 0.00997365 AN: 0.00997365

Gnomad4 NFE AF: 0.0352 AC: 0.0352177 AN: 0.0352177

Gnomad4 OTH AF: 0.0488 AC: 0.0487689 AN: 0.0487689

Alfa AF: 0.0449 Hom.: 600

Bravo AF: 0.0668

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.61
DANN	Benign	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

Publications

LitVar

Other links and lift over

dbSNP: rs1000916; hg19: chr2-31314555;