3-15453879-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005677.4(COLQ):c.1248C>A(p.Asp416Glu) variant causes a missense 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. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. D416D) has been classified as Likely benign.
Frequency
Consequence
NM_005677.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COLQ | NM_005677.4 | c.1248C>A | p.Asp416Glu | missense_variant | Exon 16 of 17 | ENST00000383788.10 | NP_005668.2 | |
COLQ | NM_080538.2 | c.1218C>A | p.Asp406Glu | missense_variant | Exon 16 of 17 | NP_536799.1 | ||
COLQ | NM_080539.4 | c.1146C>A | p.Asp382Glu | missense_variant | Exon 15 of 16 | NP_536800.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COLQ | ENST00000383788.10 | c.1248C>A | p.Asp416Glu | missense_variant | Exon 16 of 17 | 1 | NM_005677.4 | ENSP00000373298.3 | ||
COLQ | ENST00000603808.5 | c.1251C>A | p.Asp417Glu | missense_variant | Exon 16 of 17 | 1 | ENSP00000474271.1 | |||
EAF1-AS1 | ENST00000629729.2 | n.95C>A | non_coding_transcript_exon_variant | Exon 2 of 6 | 5 | ENSP00000518887.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at