2-30923631-G-T

Variant names:

• chr2-30923631-G-T
• rs10205350
• NM_024572.4:c.1380+488C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024572.4(GALNT14):​c.1380+488C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,022 control chromosomes in the GnomAD database, including 4,633 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 0.24 (4633 hom., cov: 32)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.1380+488C>A		intron_variant	Intron 13 of 14	ENST00000349752.10	NP_078848.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT14	ENST00000349752.10	c.1380+488C>A		intron_variant	Intron 13 of 14	1	NM_024572.4	ENSP00000288988.6

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36271 AN: 151904 Hom.: 4622 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.239 AC: 36326 AN: 152022 Hom.: 4633 Cov.: 32 AF XY: 0.238 AC XY: 17705 AN XY: 74330

African (AFR) AF: 0.292 AC: 12115 AN: 41440

American (AMR) AF: 0.184 AC: 2806 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 706 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2036 AN: 5140

South Asian (SAS) AF: 0.356 AC: 1715 AN: 4812

European-Finnish (FIN) AF: 0.191 AC: 2017 AN: 10580

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.208 AC: 14168 AN: 67974

Other (OTH) AF: 0.233 AC: 492 AN: 2114

Alfa AF: 0.225 Hom.: 14853

Bravo AF: 0.239

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.055
DANN	Benign	0.65
PhyloP100		-0.91
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: rs10205350; hg19: chr2-31146497;