rs149027201
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001111125.3(IQSEC2):āc.1592G>Cā(p.Arg531Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000303 in 1,210,403 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 113 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R531Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001111125.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQSEC2 | NM_001111125.3 | c.1592G>C | p.Arg531Pro | missense_variant | 5/15 | ENST00000642864.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQSEC2 | ENST00000642864.1 | c.1592G>C | p.Arg531Pro | missense_variant | 5/15 | NM_001111125.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000303 AC: 34AN: 112170Hom.: 0 Cov.: 23 AF XY: 0.000408 AC XY: 14AN XY: 34332
GnomAD3 exomes AF: 0.000401 AC: 73AN: 182224Hom.: 0 AF XY: 0.000328 AC XY: 22AN XY: 67106
GnomAD4 exome AF: 0.000303 AC: 333AN: 1098180Hom.: 0 Cov.: 33 AF XY: 0.000272 AC XY: 99AN XY: 363546
GnomAD4 genome AF: 0.000303 AC: 34AN: 112223Hom.: 0 Cov.: 23 AF XY: 0.000407 AC XY: 14AN XY: 34397
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 06, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | IQSEC2: PP2, BS2 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 25, 2016 | - - |
Intellectual disability, X-linked 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at