chr21-44077712-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003274.5(TRAPPC10):c.1397T>C(p.Ile466Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000234 in 1,454,090 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I466F) has been classified as Uncertain significance.
Frequency
Consequence
NM_003274.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC10 | NM_003274.5 | c.1397T>C | p.Ile466Thr | missense_variant | 11/23 | ENST00000291574.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC10 | ENST00000291574.9 | c.1397T>C | p.Ile466Thr | missense_variant | 11/23 | 1 | NM_003274.5 | P1 | |
TRAPPC10 | ENST00000422875.5 | c.*715T>C | 3_prime_UTR_variant, NMD_transcript_variant | 12/24 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248276Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134356
GnomAD4 exome AF: 0.0000234 AC: 34AN: 1454090Hom.: 0 Cov.: 29 AF XY: 0.0000221 AC XY: 16AN XY: 723092
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1397T>C (p.I466T) alteration is located in exon 11 (coding exon 11) of the TRAPPC10 gene. This alteration results from a T to C substitution at nucleotide position 1397, causing the isoleucine (I) at amino acid position 466 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at