rs148523016
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The XM_011517326.3(TRAPPC9):c.160A>G(p.Ser54Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000424 in 1,590,156 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
XM_011517326.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC9 | XM_011517326.3 | c.160A>G | p.Ser54Gly | missense_variant | 1/22 | ||
TRAPPC9 | XM_011517328.3 | c.160A>G | p.Ser54Gly | missense_variant | 1/22 | ||
TRAPPC9 | XM_047422294.1 | c.160A>G | p.Ser54Gly | missense_variant | 1/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC9 | ENST00000648948.2 | c.-135A>G | 5_prime_UTR_variant | 1/23 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000545 AC: 81AN: 148746Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00161 AC: 341AN: 212190Hom.: 1 AF XY: 0.00167 AC XY: 192AN XY: 115232
GnomAD4 exome AF: 0.000412 AC: 594AN: 1441316Hom.: 3 Cov.: 34 AF XY: 0.000428 AC XY: 306AN XY: 715366
GnomAD4 genome ? AF: 0.000544 AC: 81AN: 148840Hom.: 0 Cov.: 31 AF XY: 0.000686 AC XY: 50AN XY: 72844
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 12, 2013 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2017 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Intellectual Disability, Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at