chr1-241634715-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001381853.1(CHML):c.1052G>A(p.Cys351Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,613,758 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
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHML | NM_001381853.1 | c.1052G>A | p.Cys351Tyr | missense_variant | 2/2 | ENST00000366553.3 | |
OPN3 | NM_014322.3 | c.373+5167G>A | intron_variant | ENST00000366554.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHML | ENST00000366553.3 | c.1052G>A | p.Cys351Tyr | missense_variant | 2/2 | 2 | NM_001381853.1 | P1 | |
OPN3 | ENST00000366554.3 | c.373+5167G>A | intron_variant | 1 | NM_014322.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251286Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135792
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461722Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 727154
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152036Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.1052G>A (p.C351Y) alteration is located in exon 1 (coding exon 1) of the CHML gene. This alteration results from a G to A substitution at nucleotide position 1052, causing the cysteine (C) at amino acid position 351 to be replaced by a tyrosine (Y). 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