rs2008535

Positions:

• chr2-31137814-T-A
• chr2-31137814-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000349752.10(GALNT14):​c.129+144A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,026,200 control chromosomes in the GnomAD database, including 37,596 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 0.28 (6098 hom., cov: 33)
  • Exomes 𝑓: 0.26 (31498 hom.)
• Consequence: GALNT14 ENST00000349752.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.129+144A>T		intron_variant		ENST00000349752.10	NP_078848.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNT14	ENST00000349752.10	c.129+144A>T		intron_variant		1	NM_024572.4	ENSP00000288988	P1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42807 AN: 151912 Hom.: 6082 Cov.: 33

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.274

GnomAD4 exome AF: 0.265 AC: 231241 AN: 874172 Hom.: 31498 AF XY: 0.265 AC XY: 116627 AN XY: 439696

Gnomad4 AFR exome AF: 0.336

Gnomad4 AMR exome AF: 0.261

Gnomad4 ASJ exome AF: 0.254

Gnomad4 EAS exome AF: 0.295

Gnomad4 SAS exome AF: 0.299

Gnomad4 FIN exome AF: 0.253

Gnomad4 NFE exome AF: 0.258

Gnomad4 OTH exome AF: 0.275

GnomAD4 genome AF: 0.282 AC: 42853 AN: 152028 Hom.: 6098 Cov.: 33 AF XY: 0.282 AC XY: 20950 AN XY: 74306

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.277

Alfa AF: 0.266 Hom.: 680

Bravo AF: 0.284

Asia WGS AF: 0.277 AC: 961 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.2
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2008535; hg19: chr2-31360680; COSMIC: COSV61106951;