1-147242738-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004284.6(CHD1L):āc.35A>Gā(p.Gln12Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000084 in 1,261,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q12K) has been classified as Uncertain significance.
Frequency
Consequence
NM_004284.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD1L | NM_004284.6 | c.35A>G | p.Gln12Arg | missense_variant | 1/23 | ENST00000369258.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD1L | ENST00000369258.8 | c.35A>G | p.Gln12Arg | missense_variant | 1/23 | 1 | NM_004284.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000441 AC: 67AN: 151920Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000301 AC: 1AN: 33234Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 17662
GnomAD4 exome AF: 0.0000351 AC: 39AN: 1109634Hom.: 0 Cov.: 31 AF XY: 0.0000342 AC XY: 18AN XY: 526110
GnomAD4 genome AF: 0.000441 AC: 67AN: 152030Hom.: 0 Cov.: 33 AF XY: 0.000377 AC XY: 28AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.35A>G (p.Q12R) alteration is located in exon 1 (coding exon 1) of the CHD1L gene. This alteration results from a A to G substitution at nucleotide position 35, causing the glutamine (Q) at amino acid position 12 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at