12-6578867-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP2
The NM_001273.5(CHD4):c.4960C>T(p.Pro1654Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000124 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1654T) 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD4 | NM_001273.5 | c.4960C>T | p.Pro1654Ser | missense_variant | 34/40 | ENST00000544040.7 | |
CHD4 | NM_001297553.2 | c.4939C>T | p.Pro1647Ser | missense_variant | 33/39 | ||
CHD4 | NM_001363606.2 | c.4927C>T | p.Pro1643Ser | missense_variant | 34/40 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD4 | ENST00000544040.7 | c.4960C>T | p.Pro1654Ser | missense_variant | 34/40 | 5 | NM_001273.5 | A1 | |
ENST00000501075.2 | n.100+146G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461864Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727230
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at