9-112574918-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_133465.4(KIAA1958):āc.838A>Gā(p.Ile280Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_133465.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIAA1958 | NM_133465.4 | c.838A>G | p.Ile280Val | missense_variant | 2/4 | ENST00000337530.11 | NP_597722.1 | |
KIAA1958 | NM_001287036.2 | c.838A>G | p.Ile280Val | missense_variant | 2/5 | NP_001273965.1 | ||
KIAA1958 | NM_001287038.2 | c.838A>G | p.Ile280Val | missense_variant | 2/4 | NP_001273967.1 | ||
KIAA1958 | XM_011518311.3 | c.838A>G | p.Ile280Val | missense_variant | 2/3 | XP_011516613.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIAA1958 | ENST00000337530.11 | c.838A>G | p.Ile280Val | missense_variant | 2/4 | 1 | NM_133465.4 | ENSP00000336940 | P4 | |
KIAA1958 | ENST00000536272.5 | c.838A>G | p.Ile280Val | missense_variant | 2/5 | 1 | ENSP00000440504 | A1 | ||
KIAA1958 | ENST00000374244.3 | c.838A>G | p.Ile280Val | missense_variant | 2/3 | 5 | ENSP00000363362 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250510Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135364
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461790Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727184
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74308
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 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