chrX-53234268-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001111125.3(IQSEC2):c.4418C>T(p.Pro1473Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000041 in 975,899 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P1473P) has been classified as Likely benign.
Frequency
Consequence
NM_001111125.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQSEC2 | NM_001111125.3 | c.4418C>T | p.Pro1473Leu | missense_variant | 15/15 | ENST00000642864.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQSEC2 | ENST00000642864.1 | c.4418C>T | p.Pro1473Leu | missense_variant | 15/15 | NM_001111125.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 15
GnomAD3 exomes AF: 0.0000166 AC: 1AN: 60405Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 10167
GnomAD4 exome AF: 0.00000410 AC: 4AN: 975899Hom.: 0 Cov.: 21 AF XY: 0.00000678 AC XY: 2AN XY: 294809
GnomAD4 genome Cov.: 15
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 24, 2023 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | IQSEC2: PM2, PP2 - |
Intellectual disability, X-linked 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at