12-99156-G-C
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_001170738.2(IQSEC3):c.565G>C(p.Val189Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000138 in 1,446,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V189A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001170738.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IQSEC3 | ENST00000538872.6 | c.565G>C | p.Val189Leu | missense_variant | Exon 2 of 14 | 5 | NM_001170738.2 | ENSP00000437554.1 | ||
IQSEC3 | ENST00000382841.2 | c.-65G>C | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 13 | 2 | ENSP00000372292.2 | ||||
IQSEC3 | ENST00000382841.2 | c.-65G>C | 5_prime_UTR_variant | Exon 2 of 13 | 2 | ENSP00000372292.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1446484Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1AN XY: 719920 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at