rs782439813
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001111125.3(IQSEC2):c.596C>T(p.Pro199Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,155,970 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 47 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).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IQSEC2 | NM_001111125.3 | c.596C>T | p.Pro199Leu | missense_variant | 1/15 | ENST00000642864.1 | NP_001104595.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQSEC2 | ENST00000642864.1 | c.596C>T | p.Pro199Leu | missense_variant | 1/15 | NM_001111125.3 | ENSP00000495726 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000978 AC: 11AN: 112495Hom.: 0 Cov.: 24 AF XY: 0.0000865 AC XY: 3AN XY: 34693
GnomAD3 exomes AF: 0.000127 AC: 12AN: 94850Hom.: 0 AF XY: 0.000193 AC XY: 6AN XY: 31064
GnomAD4 exome AF: 0.000112 AC: 117AN: 1043475Hom.: 0 Cov.: 31 AF XY: 0.000130 AC XY: 44AN XY: 338621
GnomAD4 genome AF: 0.0000978 AC: 11AN: 112495Hom.: 0 Cov.: 24 AF XY: 0.0000865 AC XY: 3AN XY: 34693
ClinVar
Submissions by phenotype
Intellectual disability, X-linked 1 Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 16, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 26, 2017 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 22, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at