chr12-6570921-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate
The NM_001273.5(CHD4):c.5669G>A(p.Arg1890His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,170 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1890L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001273.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHD4 | NM_001273.5 | c.5669G>A | p.Arg1890His | missense_variant | Exon 39 of 40 | ENST00000544040.7 | NP_001264.2 | |
CHD4 | NM_001297553.2 | c.5648G>A | p.Arg1883His | missense_variant | Exon 38 of 39 | NP_001284482.1 | ||
CHD4 | NM_001363606.2 | c.5639G>A | p.Arg1880His | missense_variant | Exon 39 of 40 | NP_001350535.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHD4 | ENST00000544040.7 | c.5669G>A | p.Arg1890His | missense_variant | Exon 39 of 40 | 5 | NM_001273.5 | ENSP00000440542.2 | ||
ENSG00000285238 | ENST00000644480.2 | n.*750G>A | non_coding_transcript_exon_variant | Exon 40 of 55 | ENSP00000493629.2 | |||||
ENSG00000285238 | ENST00000644480.2 | n.*750G>A | 3_prime_UTR_variant | Exon 40 of 55 | ENSP00000493629.2 | |||||
ENSG00000285238 | ENST00000646322.1 | n.10-4304G>A | intron_variant | Intron 1 of 13 | ENSP00000494949.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at