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GeneBe

rs13052277

Variant summary

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

The NM_003274.5(TRAPPC10):c.1723+752A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 123,754 control chromosomes in the GnomAD database, including 3,866 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 0.25 ( 3866 hom., cov: 27)

Consequence

TRAPPC10
NM_003274.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.473
Variant links:
Genes affected
TRAPPC10 (HGNC:11868): (trafficking protein particle complex subunit 10) The protein encoded by this gene is a transmembrane protein found in the cis-Golgi complex. The encoded protein is part of the multisubunit transport protein particle (TRAPP) complex and may be involved in vesicular transport from the endoplasmic reticulum to the Golgi. Mutations in this gene could be responsible for the Unverricht-Lundborg type of progressive myoclonus epilepsy, or for autoimmune polyglandular disease type 1. [provided by RefSeq, Jul 2008]

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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=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRAPPC10NM_003274.5 linkuse as main transcriptc.1723+752A>T intron_variant ENST00000291574.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRAPPC10ENST00000291574.9 linkuse as main transcriptc.1723+752A>T intron_variant 1 NM_003274.5 P1P48553-1
TRAPPC10ENST00000422875.5 linkuse as main transcriptc.*1041+752A>T intron_variant, NMD_transcript_variant 1
TRAPPC10ENST00000461889.1 linkuse as main transcriptn.335+752A>T intron_variant, non_coding_transcript_variant 2
TRAPPC10ENST00000481460.1 linkuse as main transcriptn.342+752A>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.248
AC:
30663
AN:
123702
Hom.:
3848
Cov.:
27
show subpopulations
Gnomad AFR
AF:
0.517
Gnomad AMI
AF:
0.246
Gnomad AMR
AF:
0.215
Gnomad ASJ
AF:
0.259
Gnomad EAS
AF:
0.237
Gnomad SAS
AF:
0.328
Gnomad FIN
AF:
0.123
Gnomad MID
AF:
0.217
Gnomad NFE
AF:
0.148
Gnomad OTH
AF:
0.232
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.248
AC:
30715
AN:
123754
Hom.:
3866
Cov.:
27
AF XY:
0.248
AC XY:
14964
AN XY:
60408
show subpopulations
Gnomad4 AFR
AF:
0.518
Gnomad4 AMR
AF:
0.215
Gnomad4 ASJ
AF:
0.259
Gnomad4 EAS
AF:
0.237
Gnomad4 SAS
AF:
0.327
Gnomad4 FIN
AF:
0.123
Gnomad4 NFE
AF:
0.148
Gnomad4 OTH
AF:
0.241
Alfa
AF:
0.205
Hom.:
285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
Cadd
Benign
0.17
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

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

Other links and lift over

dbSNP: rs13052277; hg19: chr21-45500760; COSMIC: COSV52377271; API