chr5-14143754-CCCCCGCCGCGTCCTCCGG-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_007118.4(TRIO):c.40_57delTCCTCCGGCCCCGCCGCG(p.Ser14_Ala19del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.00000607 in 988,866 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007118.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIO | ENST00000344204.9 | c.40_57delTCCTCCGGCCCCGCCGCG | p.Ser14_Ala19del | conservative_inframe_deletion | Exon 1 of 57 | 1 | NM_007118.4 | ENSP00000339299.4 | ||
TRIO | ENST00000698541.1 | c.40_57delTCCTCCGGCCCCGCCGCG | p.Ser14_Ala19del | conservative_inframe_deletion | Exon 1 of 37 | ENSP00000513786.1 | ||||
TRIO | ENST00000502816.1 | n.64_81delTCCTCCGGCCCCGCCGCG | non_coding_transcript_exon_variant | Exon 1 of 5 | 2 | |||||
TRIO | ENST00000505971.5 | n.64_81delTCCTCCGGCCCCGCCGCG | non_coding_transcript_exon_variant | Exon 1 of 4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000274 AC: 4AN: 145892Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000237 AC: 2AN: 842974Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 390414
GnomAD4 genome AF: 0.0000274 AC: 4AN: 145892Hom.: 0 Cov.: 31 AF XY: 0.0000564 AC XY: 4AN XY: 70908
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.40_57del18 (p.S14_A19del) alteration is located in exon 1 (coding exon 1) of the TRIO gene. This alteration consists of an in-frame deletion of 18 nucleotides between nucleotide positions c.40 and c.57, resulting in the deletion of <NA> residues. 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