rs2098787

Variant names:

• chr2-31073778-A-G
• rs2098787
• NM_024572.4:c.129+64180T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-31073778-A-G
• chr2-31073778-A-T

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+64180T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,992 control chromosomes in the GnomAD database, including 31,214 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 (31214 hom., cov: 32)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 3 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 = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.129+64180T>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+64180T>C		intron_variant	Intron 1 of 14	1	NM_024572.4	ENSP00000288988.6

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95117 AN: 151874 Hom.: 31155 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.627 AC: 95227 AN: 151992 Hom.: 31214 Cov.: 32 AF XY: 0.621 AC XY: 46095 AN XY: 74264

African (AFR) AF: 0.833 AC: 34554 AN: 41500

American (AMR) AF: 0.622 AC: 9500 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3468

East Asian (EAS) AF: 0.462 AC: 2383 AN: 5156

South Asian (SAS) AF: 0.493 AC: 2378 AN: 4820

European-Finnish (FIN) AF: 0.518 AC: 5450 AN: 10522

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37326 AN: 67946

Other (OTH) AF: 0.572 AC: 1205 AN: 2106

Alfa AF: 0.564 Hom.: 12367

Bravo AF: 0.642

Asia WGS AF: 0.497 AC: 1728 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	1.4
DANN	Benign	0.70
PhyloP100		-0.13
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: rs2098787; hg19: chr2-31296644;