rs1556880172
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001111125.3(IQSEC2):c.396C>T(p.Asp132=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000949 in 1,053,487 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001111125.3 synonymous
Scores
Clinical Significance
Conservation
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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.396C>T | p.Asp132= | synonymous_variant | 1/15 | ENST00000642864.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQSEC2 | ENST00000642864.1 | c.396C>T | p.Asp132= | synonymous_variant | 1/15 | NM_001111125.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 exomes AF: 0.00000925 AC: 1AN: 108068Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 38764
GnomAD4 exome AF: 9.49e-7 AC: 1AN: 1053487Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 344611
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
Intellectual disability, X-linked 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at