rs1862975

Variant names:

• chr2-31103566-A-C
• rs1862975
• NM_024572.4:c.129+34392T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-31103566-A-C
• chr2-31103566-A-G

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+34392T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,932 control chromosomes in the GnomAD database, including 30,652 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 0.62 (30652 hom., cov: 31)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.129+34392T>G		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+34392T>G		intron_variant	Intron 1 of 14	1	NM_024572.4	ENSP00000288988.6

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93849 AN: 151812 Hom.: 30602 Cov.: 31

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.618 AC: 93950 AN: 151932 Hom.: 30652 Cov.: 31 AF XY: 0.610 AC XY: 45315 AN XY: 74258

African (AFR) AF: 0.829 AC: 34396 AN: 41470

American (AMR) AF: 0.570 AC: 8687 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3466

East Asian (EAS) AF: 0.263 AC: 1358 AN: 5168

South Asian (SAS) AF: 0.486 AC: 2340 AN: 4816

European-Finnish (FIN) AF: 0.529 AC: 5584 AN: 10548

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37986 AN: 67906

Other (OTH) AF: 0.561 AC: 1184 AN: 2112

Alfa AF: 0.568 Hom.: 8412

Bravo AF: 0.627

Asia WGS AF: 0.402 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-1.4
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: rs1862975; hg19: chr2-31326432;