chr8-139730686-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001160372.4(TRAPPC9):​c.*375C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00908 in 255,454 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.010 ( 57 hom., cov: 32)
Exomes 𝑓: 0.0076 ( 38 hom. )

Consequence

TRAPPC9
NM_001160372.4 3_prime_UTR

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.139
Variant links:
Genes affected
TRAPPC9 (HGNC:30832): (trafficking protein particle complex subunit 9) This gene encodes a protein that likely plays a role in NF-kappa-B signaling. Mutations in this gene have been associated with autosomal-recessive cognitive disability. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 8-139730686-G-A is Benign according to our data. Variant chr8-139730686-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 362053.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0646 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRAPPC9NM_001160372.4 linkuse as main transcriptc.*375C>T 3_prime_UTR_variant 23/23 ENST00000438773.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRAPPC9ENST00000438773.4 linkuse as main transcriptc.*375C>T 3_prime_UTR_variant 23/231 NM_001160372.4 P1Q96Q05-1
TRAPPC9ENST00000520857.5 linkuse as main transcriptc.*375C>T 3_prime_UTR_variant 21/211
TRAPPC9ENST00000648948.2 linkuse as main transcriptc.*375C>T 3_prime_UTR_variant 23/23 P1Q96Q05-1

Frequencies

GnomAD3 genomes
AF:
0.0100
AC:
1528
AN:
152168
Hom.:
57
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00229
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0679
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0658
Gnomad SAS
AF:
0.00269
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000323
Gnomad OTH
AF:
0.00907
GnomAD4 exome
AF:
0.00764
AC:
788
AN:
103168
Hom.:
38
Cov.:
0
AF XY:
0.00765
AC XY:
406
AN XY:
53090
show subpopulations
Gnomad4 AFR exome
AF:
0.000700
Gnomad4 AMR exome
AF:
0.0589
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0748
Gnomad4 SAS exome
AF:
0.000717
Gnomad4 FIN exome
AF:
0.000457
Gnomad4 NFE exome
AF:
0.000315
Gnomad4 OTH exome
AF:
0.00500
GnomAD4 genome
AF:
0.0101
AC:
1532
AN:
152286
Hom.:
57
Cov.:
32
AF XY:
0.0118
AC XY:
876
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.00229
Gnomad4 AMR
AF:
0.0680
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0663
Gnomad4 SAS
AF:
0.00269
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.000323
Gnomad4 OTH
AF:
0.00898
Alfa
AF:
0.00381
Hom.:
0
Bravo
AF:
0.0140
Asia WGS
AF:
0.0250
AC:
88
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Intellectual Disability, Recessive Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
3.5
DANN
Benign
0.44

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: rs79408026; hg19: chr8-140742929; API