19-18257185-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001145304.2(IQCN):āc.4099A>Gā(p.Ile1367Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,612,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001145304.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCN | NM_001145304.2 | c.4099A>G | p.Ile1367Val | missense_variant | 4/4 | ENST00000392413.5 | |
IQCN | NM_025249.4 | c.3538A>G | p.Ile1180Val | missense_variant | 4/4 | ||
IQCN | NM_001145305.2 | c.3400A>G | p.Ile1134Val | missense_variant | 4/4 | ||
IQCN | XM_005260084.2 | c.4099A>G | p.Ile1367Val | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCN | ENST00000392413.5 | c.4099A>G | p.Ile1367Val | missense_variant | 4/4 | 1 | NM_001145304.2 | A2 | |
IQCN | ENST00000600328.7 | c.3538A>G | p.Ile1180Val | missense_variant | 4/4 | 1 | P2 | ||
IQCN | ENST00000600359.7 | c.3400A>G | p.Ile1134Val | missense_variant | 4/4 | 2 | A2 | ||
IQCN | ENST00000599638.2 | n.5434A>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250112Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135424
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460504Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726614
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74382
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at