chr2-31024619-T-C

Variant names:

• chr2-31024619-T-C
• rs6752303
• NM_024572.4:c.130-31612A>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.130-31612A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,034 control chromosomes in the GnomAD database, including 14,437 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 0.43 (14437 hom., cov: 32)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 8 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024572.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT14	NM_024572.4	MANE Select	c.130-31612A>G		intron	N/A	NP_078848.2	Q96FL9-1
	GALNT14	NM_001253826.2		c.315-58317A>G		intron	N/A	NP_001240755.1	Q96FL9-3
	GALNT14	NM_001253827.2		c.70-31612A>G		intron	N/A	NP_001240756.1	Q96FL9-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GALNT14	ENST00000349752.10	TSL:1 MANE Select	c.130-31612A>G		intron	N/A	ENSP00000288988.6	Q96FL9-1
	GALNT14	ENST00000464038.5	TSL:1	n.389-31612A>G		intron	N/A
	GALNT14	ENST00000324589.9	TSL:2	c.315-58317A>G		intron	N/A	ENSP00000314500.5	Q96FL9-3

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65691 AN: 151914 Hom.: 14416 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.433 AC: 65760 AN: 152034 Hom.: 14437 Cov.: 32 AF XY: 0.429 AC XY: 31907 AN XY: 74332

African (AFR) AF: 0.473 AC: 19632 AN: 41470

American (AMR) AF: 0.519 AC: 7916 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1504 AN: 3472

East Asian (EAS) AF: 0.557 AC: 2874 AN: 5160

South Asian (SAS) AF: 0.345 AC: 1659 AN: 4810

European-Finnish (FIN) AF: 0.341 AC: 3605 AN: 10570

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27166 AN: 67974

Other (OTH) AF: 0.413 AC: 871 AN: 2110

Alfa AF: 0.415 Hom.: 17416

Bravo AF: 0.450

Asia WGS AF: 0.445 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.57
PhyloP100		-1.3
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: rs6752303; hg19: chr2-31247485;