2-31105946-T-G

Variant names:

• chr2-31105946-T-G
• rs13029054
• NM_024572.4:c.129+32012A>C

Variant summary

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

The NM_024572.4(GALNT14):​c.129+32012A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,884 control chromosomes in the GnomAD database, including 28,464 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 0.60 (28464 hom., cov: 31)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.951

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.129+32012A>C		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+32012A>C		intron_variant	Intron 1 of 14	1	NM_024572.4	ENSP00000288988.6

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90892 AN: 151764 Hom.: 28421 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.599 AC: 90984 AN: 151884 Hom.: 28464 Cov.: 31 AF XY: 0.592 AC XY: 43947 AN XY: 74248

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.545

Alfa AF: 0.439 Hom.: 1105

Bravo AF: 0.606

Asia WGS AF: 0.400 AC: 1393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.72

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: rs13029054; hg19: chr2-31328812;