chr8-139730686-G-A
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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
NM_001160372.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.139
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]
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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 |
---|---|---|---|---|---|---|---|
TRAPPC9 | NM_001160372.4 | c.*375C>T | 3_prime_UTR_variant | 23/23 | ENST00000438773.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC9 | ENST00000438773.4 | c.*375C>T | 3_prime_UTR_variant | 23/23 | 1 | NM_001160372.4 | P1 | ||
TRAPPC9 | ENST00000520857.5 | c.*375C>T | 3_prime_UTR_variant | 21/21 | 1 | ||||
TRAPPC9 | ENST00000648948.2 | c.*375C>T | 3_prime_UTR_variant | 23/23 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0100 AC: 1528AN: 152168Hom.: 57 Cov.: 32
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GnomAD4 exome AF: 0.00764 AC: 788AN: 103168Hom.: 38 Cov.: 0 AF XY: 0.00765 AC XY: 406AN XY: 53090
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GnomAD4 genome AF: 0.0101 AC: 1532AN: 152286Hom.: 57 Cov.: 32 AF XY: 0.0118 AC XY: 876AN XY: 74454
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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 submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at