rs2098787

chr2-31073778-A-Gchr2-31073778-A-T

Variant summary

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

The NM_024572.4(GALNT14):c.129+64180T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,992 control chromosomes in the GnomAD database, including 31,214 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 (31214 hom., cov: 32)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT14	NM_024572.4	c.129+64180T>C		intron_variant		ENST00000349752.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT14	ENST00000349752.10	c.129+64180T>C		intron_variant		1	NM_024572.4	P1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95117 AN: 151874 Hom.: 31155 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.627 AC: 95227 AN: 151992 Hom.: 31214 Cov.: 32 AF XY: 0.621 AC XY: 46095 AN XY: 74264

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.572

Alfa AF: 0.565 Hom.: 11173

Bravo AF: 0.642

Asia WGS AF: 0.497 AC: 1728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.70

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: rs2098787; hg19: chr2-31296644;