chr21-44012513-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_003274.5(TRAPPC10):c.20C>T(p.Pro7Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00071 in 1,530,952 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003274.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC10 | NM_003274.5 | c.20C>T | p.Pro7Leu | missense_variant | 1/23 | ENST00000291574.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC10 | ENST00000291574.9 | c.20C>T | p.Pro7Leu | missense_variant | 1/23 | 1 | NM_003274.5 | P1 | |
TRAPPC10 | ENST00000380221.7 | c.20C>T | p.Pro7Leu | missense_variant | 1/7 | 1 | |||
TRAPPC10 | ENST00000422875.5 | c.20C>T | p.Pro7Leu | missense_variant, NMD_transcript_variant | 1/24 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00104 AC: 157AN: 151476Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00105 AC: 144AN: 137348Hom.: 1 AF XY: 0.000983 AC XY: 73AN XY: 74242
GnomAD4 exome AF: 0.000674 AC: 930AN: 1379368Hom.: 6 Cov.: 30 AF XY: 0.000711 AC XY: 484AN XY: 680558
GnomAD4 genome ? AF: 0.00104 AC: 157AN: 151584Hom.: 0 Cov.: 32 AF XY: 0.00134 AC XY: 99AN XY: 74090
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2022 | The c.20C>T (p.P7L) alteration is located in exon 1 (coding exon 1) of the TRAPPC10 gene. This alteration results from a C to T substitution at nucleotide position 20, causing the proline (P) at amino acid position 7 to be replaced by a leucine (L). 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