chr1-241634326-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001381853.1(CHML):c.1441C>G(p.Pro481Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001381853.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHML | NM_001381853.1 | c.1441C>G | p.Pro481Ala | missense_variant | 2/2 | ENST00000366553.3 | |
OPN3 | NM_014322.3 | c.373+5556C>G | intron_variant | ENST00000366554.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHML | ENST00000366553.3 | c.1441C>G | p.Pro481Ala | missense_variant | 2/2 | 2 | NM_001381853.1 | P1 | |
OPN3 | ENST00000366554.3 | c.373+5556C>G | intron_variant | 1 | NM_014322.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250786Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135522
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461686Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 727146
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 01, 2023 | The c.1441C>G (p.P481A) alteration is located in exon 1 (coding exon 1) of the CHML gene. This alteration results from a C to G substitution at nucleotide position 1441, causing the proline (P) at amino acid position 481 to be replaced by an alanine (A). 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