2-31074658-T-G

Variant names:

• chr2-31074658-T-G
• rs1862981
• NM_024572.4:c.129+63300A>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+63300A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,796 control chromosomes in the GnomAD database, including 31,177 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 (31177 hom., cov: 30)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.129+63300A>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+63300A>C		intron_variant	Intron 1 of 14	1	NM_024572.4	ENSP00000288988.6

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95175 AN: 151678 Hom.: 31125 Cov.: 30

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.628 AC: 95278 AN: 151796 Hom.: 31177 Cov.: 30 AF XY: 0.622 AC XY: 46110 AN XY: 74162

African (AFR) AF: 0.825 AC: 34161 AN: 41424

American (AMR) AF: 0.622 AC: 9502 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1704 AN: 3462

East Asian (EAS) AF: 0.460 AC: 2362 AN: 5138

South Asian (SAS) AF: 0.495 AC: 2372 AN: 4790

European-Finnish (FIN) AF: 0.525 AC: 5516 AN: 10506

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37726 AN: 67898

Other (OTH) AF: 0.574 AC: 1212 AN: 2110

Alfa AF: 0.571 Hom.: 41318

Bravo AF: 0.643

Asia WGS AF: 0.493 AC: 1716 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	1.8
DANN	Benign	0.79
PhyloP100		-0.28
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: rs1862981; hg19: chr2-31297524;