rs1556863213
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001111125.3(IQSEC2):c.1849C>T(p.Arg617Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000355 in 1,210,020 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R617H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001111125.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQSEC2 | NM_001111125.3 | c.1849C>T | p.Arg617Cys | missense_variant | 5/15 | ENST00000642864.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQSEC2 | ENST00000642864.1 | c.1849C>T | p.Arg617Cys | missense_variant | 5/15 | NM_001111125.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000267 AC: 3AN: 112516Hom.: 0 Cov.: 23 AF XY: 0.0000289 AC XY: 1AN XY: 34658
GnomAD3 exomes AF: 0.0000112 AC: 2AN: 179033Hom.: 0 AF XY: 0.0000155 AC XY: 1AN XY: 64703
GnomAD4 exome AF: 0.0000364 AC: 40AN: 1097504Hom.: 0 Cov.: 33 AF XY: 0.0000496 AC XY: 18AN XY: 362940
GnomAD4 genome ? AF: 0.0000267 AC: 3AN: 112516Hom.: 0 Cov.: 23 AF XY: 0.0000289 AC XY: 1AN XY: 34658
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 02, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2021 | - - |
Intellectual disability, X-linked 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 13, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at