chrX-110694255-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001143981.2(CHRDL1):c.686C>T(p.Ala229Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 1,207,285 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001143981.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRDL1 | NM_001143981.2 | c.686C>T | p.Ala229Val | missense_variant | 8/12 | ENST00000372042.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRDL1 | ENST00000372042.6 | c.686C>T | p.Ala229Val | missense_variant | 8/12 | 2 | NM_001143981.2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000152 AC: 17AN: 112090Hom.: 0 Cov.: 23 AF XY: 0.000117 AC XY: 4AN XY: 34270
GnomAD3 exomes AF: 0.0000327 AC: 6AN: 183242Hom.: 0 AF XY: 0.0000738 AC XY: 5AN XY: 67710
GnomAD4 exome AF: 0.00000730 AC: 8AN: 1095143Hom.: 0 Cov.: 29 AF XY: 0.00000555 AC XY: 2AN XY: 360633
GnomAD4 genome AF: 0.000152 AC: 17AN: 112142Hom.: 0 Cov.: 23 AF XY: 0.000117 AC XY: 4AN XY: 34332
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2022 | The c.686C>T (p.A229V) alteration is located in exon 8 (coding exon 7) of the CHRDL1 gene. This alteration results from a C to T substitution at nucleotide position 686, causing the alanine (A) at amino acid position 229 to be replaced by a valine (V). 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