rs797045629
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001111125.3(IQSEC2):c.3663A>G(p.Pro1221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000405 in 1,159,908 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 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 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQSEC2 | NM_001111125.3 | c.3663A>G | p.Pro1221= | synonymous_variant | 15/15 | ENST00000642864.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQSEC2 | ENST00000642864.1 | c.3663A>G | p.Pro1221= | synonymous_variant | 15/15 | NM_001111125.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000282 AC: 3AN: 106471Hom.: 0 Cov.: 21 AF XY: 0.0000333 AC XY: 1AN XY: 30019
GnomAD3 exomes AF: 0.0000532 AC: 6AN: 112811Hom.: 0 AF XY: 0.0000740 AC XY: 3AN XY: 40525
GnomAD4 exome AF: 0.0000418 AC: 44AN: 1053437Hom.: 0 Cov.: 47 AF XY: 0.0000435 AC XY: 15AN XY: 344487
GnomAD4 genome ? AF: 0.0000282 AC: 3AN: 106471Hom.: 0 Cov.: 21 AF XY: 0.0000333 AC XY: 1AN XY: 30019
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 06, 2015 | - - |
Intellectual disability, X-linked 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 20, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at