chr1-6110524-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP2PP3_Strong
The NM_015557.3(CHD5):c.5252A>G(p.His1751Arg) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015557.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD5 | NM_015557.3 | c.5252A>G | p.His1751Arg | missense_variant, splice_region_variant | 37/42 | ENST00000262450.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD5 | ENST00000262450.8 | c.5252A>G | p.His1751Arg | missense_variant, splice_region_variant | 37/42 | 1 | NM_015557.3 | P1 | |
CHD5 | ENST00000462991.5 | c.*324A>G | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 27/31 | 1 | ||||
CHD5 | ENST00000377999.5 | c.*1822A>G | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 17/21 | 2 | ||||
CHD5 | ENST00000496404.1 | c.*292A>G | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 29/34 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 38
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center | May 02, 2023 | PM2, PP2, PP3 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.