chr19-18257388-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.3896G>A(p.Arg1299His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,611,194 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 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.3896G>A | p.Arg1299His | missense_variant | 4/4 | ENST00000392413.5 | |
IQCN | NM_025249.4 | c.3335G>A | p.Arg1112His | missense_variant | 4/4 | ||
IQCN | NM_001145305.2 | c.3197G>A | p.Arg1066His | missense_variant | 4/4 | ||
IQCN | XM_005260084.2 | c.3896G>A | p.Arg1299His | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCN | ENST00000392413.5 | c.3896G>A | p.Arg1299His | missense_variant | 4/4 | 1 | NM_001145304.2 | A2 | |
IQCN | ENST00000600328.7 | c.3335G>A | p.Arg1112His | missense_variant | 4/4 | 1 | P2 | ||
IQCN | ENST00000600359.7 | c.3197G>A | p.Arg1066His | missense_variant | 4/4 | 2 | A2 | ||
IQCN | ENST00000599638.2 | n.5231G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000969 AC: 24AN: 247610Hom.: 1 AF XY: 0.0000818 AC XY: 11AN XY: 134506
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1458874Hom.: 1 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 725740
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at