rs2303324

chr2-30966370-G-Achr2-30966370-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024572.4(GALNT14):c.300-68C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,180,702 control chromosomes in the GnomAD database, including 15,915 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 0.16 (1953 hom., cov: 32)
  • Exomes 𝑓: 0.16 (13962 hom.)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT14	NM_024572.4	c.300-68C>T		intron_variant		ENST00000349752.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT14	ENST00000349752.10	c.300-68C>T		intron_variant		1	NM_024572.4	P1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23644 AN: 151966 Hom.: 1953 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.159 AC: 163727 AN: 1028618 Hom.: 13962 AF XY: 0.159 AC XY: 83679 AN XY: 526508

Gnomad4 AFR exome AF: 0.166

Gnomad4 AMR exome AF: 0.134

Gnomad4 ASJ exome AF: 0.0717

Gnomad4 EAS exome AF: 0.348

Gnomad4 SAS exome AF: 0.159

Gnomad4 FIN exome AF: 0.152

Gnomad4 NFE exome AF: 0.155

Gnomad4 OTH exome AF: 0.145

GnomAD4 genome AF: 0.156 AC: 23657 AN: 152084 Hom.: 1953 Cov.: 32 AF XY: 0.154 AC XY: 11478 AN XY: 74330

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0686

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.135

Alfa AF: 0.154 Hom.: 620

Bravo AF: 0.156

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.023
Dann	Benign	0.28

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: rs2303324; hg19: chr2-31189236; COSMIC: COSV61103323;