chr22-41235303-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138481.2(CHADL):c.2104G>A(p.Ala702Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,550,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138481.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHADL | ENST00000216241.14 | c.2104G>A | p.Ala702Thr | missense_variant | Exon 5 of 6 | 1 | NM_138481.2 | ENSP00000216241.9 | ||
CHADL | ENST00000455425.1 | c.595G>A | p.Ala199Thr | missense_variant | Exon 4 of 4 | 2 | ENSP00000412359.1 | |||
CHADL | ENST00000417999.5 | c.1974-107G>A | intron_variant | Intron 3 of 4 | 5 | ENSP00000392046.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000648 AC: 1AN: 154424Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82100
GnomAD4 exome AF: 0.0000150 AC: 21AN: 1398686Hom.: 0 Cov.: 31 AF XY: 0.0000130 AC XY: 9AN XY: 689814
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2104G>A (p.A702T) alteration is located in exon 5 (coding exon 5) of the CHADL gene. This alteration results from a G to A substitution at nucleotide position 2104, causing the alanine (A) at amino acid position 702 to be replaced by a threonine (T). 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