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rs1862975

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024572.4(GALNT14):c.129+34392T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,932 control chromosomes in the GnomAD database, including 30,652 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 0.62 ( 30652 hom., cov: 31)

Consequence

GALNT14
NM_024572.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GALNT14NM_024572.4 linkuse as main transcriptc.129+34392T>G intron_variant ENST00000349752.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GALNT14ENST00000349752.10 linkuse as main transcriptc.129+34392T>G intron_variant 1 NM_024572.4 P1Q96FL9-1

Frequencies

GnomAD3 genomes
AF:
0.618
AC:
93849
AN:
151812
Hom.:
30602
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.829
Gnomad AMI
AF:
0.585
Gnomad AMR
AF:
0.570
Gnomad ASJ
AF:
0.488
Gnomad EAS
AF:
0.264
Gnomad SAS
AF:
0.486
Gnomad FIN
AF:
0.529
Gnomad MID
AF:
0.655
Gnomad NFE
AF:
0.559
Gnomad OTH
AF:
0.564
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.618
AC:
93950
AN:
151932
Hom.:
30652
Cov.:
31
AF XY:
0.610
AC XY:
45315
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.829
Gnomad4 AMR
AF:
0.570
Gnomad4 ASJ
AF:
0.488
Gnomad4 EAS
AF:
0.263
Gnomad4 SAS
AF:
0.486
Gnomad4 FIN
AF:
0.529
Gnomad4 NFE
AF:
0.559
Gnomad4 OTH
AF:
0.561
Alfa
AF:
0.553
Hom.:
4746
Bravo
AF:
0.627
Asia WGS
AF:
0.402
AC:
1401
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
Cadd
Benign
1.1
Dann
Benign
0.61

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1862975; hg19: chr2-31326432; API