rs750014782
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP5BS2
The NM_016139.4(CHCHD2):c.300+5G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000822 in 1,459,368 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (no stars).
Frequency
Consequence
NM_016139.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHCHD2 | NM_016139.4 | c.300+5G>A | splice_region_variant, intron_variant | ENST00000395422.4 | NP_057223.1 | |||
CHCHD2 | NM_001320327.2 | c.300+5G>A | splice_region_variant, intron_variant | NP_001307256.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHCHD2 | ENST00000395422.4 | c.300+5G>A | splice_region_variant, intron_variant | 1 | NM_016139.4 | ENSP00000378812.3 | ||||
CHCHD2 | ENST00000473095.1 | n.318+5G>A | splice_region_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249734Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135162
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1459368Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 725514
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Parkinson disease 22, autosomal dominant Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at