chr19-18257689-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001145304.2(IQCN):c.3595G>A(p.Gly1199Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000443 in 1,604,162 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 (★).
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.3595G>A | p.Gly1199Arg | missense_variant | 4/4 | ENST00000392413.5 | |
IQCN | NM_025249.4 | c.3034G>A | p.Gly1012Arg | missense_variant | 4/4 | ||
IQCN | NM_001145305.2 | c.2896G>A | p.Gly966Arg | missense_variant | 4/4 | ||
IQCN | XM_005260084.2 | c.3595G>A | p.Gly1199Arg | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCN | ENST00000392413.5 | c.3595G>A | p.Gly1199Arg | missense_variant | 4/4 | 1 | NM_001145304.2 | A2 | |
IQCN | ENST00000600328.7 | c.3034G>A | p.Gly1012Arg | missense_variant | 4/4 | 1 | P2 | ||
IQCN | ENST00000600359.7 | c.2896G>A | p.Gly966Arg | missense_variant | 4/4 | 2 | A2 | ||
IQCN | ENST00000599638.2 | n.4930G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000415 AC: 10AN: 240788Hom.: 0 AF XY: 0.0000304 AC XY: 4AN XY: 131532
GnomAD4 exome AF: 0.0000344 AC: 50AN: 1451946Hom.: 0 Cov.: 30 AF XY: 0.0000347 AC XY: 25AN XY: 720882
GnomAD4 genome AF: 0.000138 AC: 21AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74366
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at