rs104894193
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_021926.4(ALX4):c.653G>A(p.Arg218Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_021926.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALX4 | NM_021926.4 | c.653G>A | p.Arg218Gln | missense_variant | 2/4 | ENST00000652299.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALX4 | ENST00000652299.1 | c.653G>A | p.Arg218Gln | missense_variant | 2/4 | NM_021926.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251470Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135912
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461710Hom.: 0 Cov.: 35 AF XY: 0.00000413 AC XY: 3AN XY: 727160
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Parietal foramina 2 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2006 | - - |
Pathogenic, no assertion criteria provided | curation | GeneReviews | Nov 08, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at