rs2365200

Variant names:

• chr2-31093660-A-G
• rs2365200
• NM_024572.4:c.129+44298T>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+44298T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 152,152 control chromosomes in the GnomAD database, including 29,150 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 (29150 hom., cov: 33)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• 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=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.129+44298T>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+44298T>C		intron_variant	Intron 1 of 14	1	NM_024572.4	ENSP00000288988.6

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91862 AN: 152034 Hom.: 29117 Cov.: 33

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.604 AC: 91947 AN: 152152 Hom.: 29150 Cov.: 33 AF XY: 0.596 AC XY: 44295 AN XY: 74376

African (AFR) AF: 0.793 AC: 32929 AN: 41530

American (AMR) AF: 0.563 AC: 8612 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3468

East Asian (EAS) AF: 0.250 AC: 1292 AN: 5170

South Asian (SAS) AF: 0.483 AC: 2331 AN: 4828

European-Finnish (FIN) AF: 0.494 AC: 5222 AN: 10570

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

European-Non Finnish (NFE) AF: 0.559 AC: 37977 AN: 67982

Other (OTH) AF: 0.551 AC: 1165 AN: 2114

Alfa AF: 0.568 Hom.: 13822

Bravo AF: 0.614

Asia WGS AF: 0.397 AC: 1383 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	19
DANN	Benign	0.62
PhyloP100		0.53
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: rs2365200; hg19: chr2-31316526;