1-165752099-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_019026.6(TMCO1):c.323+3G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_019026.6 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMCO1 | NM_019026.6 | c.323+3G>C | splice_region_variant, intron_variant | Intron 5 of 6 | ENST00000367881.11 | NP_061899.3 | ||
TMCO1 | NM_001256164.1 | c.374+3G>C | splice_region_variant, intron_variant | Intron 5 of 6 | NP_001243093.1 | |||
TMCO1 | NM_001256165.1 | c.287+3G>C | splice_region_variant, intron_variant | Intron 5 of 6 | NP_001243094.1 | |||
TMCO1 | NR_045818.1 | n.417+3G>C | splice_region_variant, intron_variant | Intron 5 of 6 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1 Pathogenic:1
Homozygous variant in a Turkish individual; RNA demonstrates missplicing due to intronic variant (Skipping of exon 5) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at