2-30967907-A-G

Variant names:

• chr2-30967907-A-G
• rs12617790
• NM_024572.4:c.300-1605T>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.300-1605T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,986 control chromosomes in the GnomAD database, including 9,810 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 0.31 (9810 hom., cov: 32)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.300-1605T>C		intron_variant	Intron 2 of 14	ENST00000349752.10	NP_078848.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GALNT14	ENST00000349752.10	c.300-1605T>C		intron_variant	Intron 2 of 14	1	NM_024572.4	ENSP00000288988.6

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47646 AN: 151868 Hom.: 9761 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.314 AC: 47751 AN: 151986 Hom.: 9810 Cov.: 32 AF XY: 0.313 AC XY: 23248 AN XY: 74290

African (AFR) AF: 0.564 AC: 23352 AN: 41434

American (AMR) AF: 0.245 AC: 3745 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0998 AC: 346 AN: 3466

East Asian (EAS) AF: 0.594 AC: 3059 AN: 5150

South Asian (SAS) AF: 0.303 AC: 1461 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2211 AN: 10556

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.189 AC: 12833 AN: 67952

Other (OTH) AF: 0.267 AC: 565 AN: 2114

Alfa AF: 0.195 Hom.: 1929

Bravo AF: 0.330

Asia WGS AF: 0.457 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.49
DANN	Benign	0.64
PhyloP100		-1.0
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: rs12617790; hg19: chr2-31190773;