chr2-31024619-T-C

Position:

• chr2-31024619-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GALNT14	NM_024572.4	c.130-31612A>G		intron_variant		ENST00000349752.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GALNT14	ENST00000349752.10	c.130-31612A>G		intron_variant		1	NM_024572.4	P1

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

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.413

Alfa AF: 0.404 Hom.: 1703

Bravo AF: 0.450

Asia WGS AF: 0.445 AC: 1545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.30
DANN	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs6752303; hg19: chr2-31247485;