2-31105946-T-G

Variant names:

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

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+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
• Publications: 1 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=-0.87).
• 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

African (AFR) AF: 0.777 AC: 32192 AN: 41412

American (AMR) AF: 0.563 AC: 8596 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1689 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1311 AN: 5160

South Asian (SAS) AF: 0.484 AC: 2327 AN: 4812

European-Finnish (FIN) AF: 0.523 AC: 5521 AN: 10548

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37482 AN: 67908

Other (OTH) AF: 0.545 AC: 1149 AN: 2110

Alfa AF: 0.466 Hom.: 1343

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
PhyloP100		0.95
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

Other links and lift over

dbSNP: rs13029054; hg19: chr2-31328812;