chr1-147242777-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004284.6(CHD1L):āc.74G>Cā(p.Arg25Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 1,269,940 control chromosomes in the GnomAD database, including 5,842 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004284.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD1L | NM_004284.6 | c.74G>C | p.Arg25Pro | missense_variant | 1/23 | ENST00000369258.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD1L | ENST00000369258.8 | c.74G>C | p.Arg25Pro | missense_variant | 1/23 | 1 | NM_004284.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0922 AC: 14027AN: 152100Hom.: 717 Cov.: 33
GnomAD3 exomes AF: 0.120 AC: 5269AN: 43920Hom.: 329 AF XY: 0.120 AC XY: 2710AN XY: 22556
GnomAD4 exome AF: 0.0912 AC: 101986AN: 1117732Hom.: 5120 Cov.: 33 AF XY: 0.0915 AC XY: 48522AN XY: 530552
GnomAD4 genome AF: 0.0922 AC: 14039AN: 152208Hom.: 722 Cov.: 33 AF XY: 0.0948 AC XY: 7053AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at