12-120504087-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032314.4(COQ5):c.771-6G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000117 in 1,538,074 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_032314.4 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
COQ5 | NM_032314.4 | c.771-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000288532.11 | |||
COQ5 | XM_006719639.3 | c.528-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COQ5 | ENST00000288532.11 | c.771-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_032314.4 | P1 | |||
COQ5 | ENST00000445328.6 | c.549-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
COQ5 | ENST00000552443.5 | c.528-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000123 AC: 17AN: 1385968Hom.: 1 Cov.: 23 AF XY: 0.00000865 AC XY: 6AN XY: 694036
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74296
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 02, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at