chrX-53248188-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001111125.3(IQSEC2):āc.2508G>Cā(p.Ala836=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000912 in 1,096,449 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001111125.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IQSEC2 | NM_001111125.3 | c.2508G>C | p.Ala836= | synonymous_variant | 7/15 | ENST00000642864.1 | NP_001104595.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQSEC2 | ENST00000642864.1 | c.2508G>C | p.Ala836= | synonymous_variant | 7/15 | NM_001111125.3 | ENSP00000495726 | P1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome AF: 9.12e-7 AC: 1AN: 1096449Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 1AN XY: 361857
GnomAD4 genome Cov.: 22
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at