rs11676188

Positions:

• chr2-31129922-C-G

Variant summary

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

The NM_024572.4(GALNT14):​c.129+8036G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,144 control chromosomes in the GnomAD database, including 2,577 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 0.17 (2577 hom., cov: 32)
• Consequence: GALNT14 NM_024572.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNT14	NM_024572.4	c.129+8036G>C		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+8036G>C		intron_variant		1	NM_024572.4	ENSP00000288988	P1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26357 AN: 152026 Hom.: 2571 Cov.: 32

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.173 AC: 26377 AN: 152144 Hom.: 2577 Cov.: 32 AF XY: 0.174 AC XY: 12958 AN XY: 74366

Gnomad4 AFR AF: 0.0983

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.182

Alfa AF: 0.190 Hom.: 395

Bravo AF: 0.165

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.24

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: rs11676188; hg19: chr2-31352788;