chr3-159262580-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001042706.3(IQCJ):c.188G>A(p.Arg63Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000775 in 1,613,684 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R63W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001042706.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCJ | NM_001042706.3 | c.188G>A | p.Arg63Gln | missense_variant | 4/4 | ENST00000397832.7 | |
IQCJ-SCHIP1 | NM_001197113.2 | c.188G>A | p.Arg63Gln | missense_variant | 4/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCJ | ENST00000397832.7 | c.188G>A | p.Arg63Gln | missense_variant | 4/4 | 1 | NM_001042706.3 | ||
IQCJ | ENST00000451172.5 | c.188G>A | p.Arg63Gln | missense_variant | 4/5 | 1 | P1 | ||
IQCJ | ENST00000482126.1 | c.107G>A | p.Arg36Gln | missense_variant | 3/4 | 1 | |||
IQCJ | ENST00000481796.1 | n.468G>A | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000847 AC: 21AN: 247884Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 134594
GnomAD4 exome AF: 0.0000801 AC: 117AN: 1461498Hom.: 0 Cov.: 32 AF XY: 0.0000867 AC XY: 63AN XY: 727010
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.188G>A (p.R63Q) alteration is located in exon 4 (coding exon 4) of the IQCJ gene. This alteration results from a G to A substitution at nucleotide position 188, causing the arginine (R) at amino acid position 63 to be replaced by a glutamine (Q). 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