chr7-138837928-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001164665.2(KIAA1549):c.5831C>T(p.Thr1944Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,461,462 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T1944T) has been classified as Likely benign.
Frequency
Consequence
NM_001164665.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA1549 | NM_001164665.2 | c.5831C>T | p.Thr1944Ile | missense_variant | 20/20 | ENST00000422774.2 | |
KIAA1549 | NM_020910.3 | c.5783C>T | p.Thr1928Ile | missense_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA1549 | ENST00000422774.2 | c.5831C>T | p.Thr1944Ile | missense_variant | 20/20 | 1 | NM_001164665.2 | A2 | |
KIAA1549 | ENST00000440172.5 | c.5783C>T | p.Thr1928Ile | missense_variant | 20/20 | 1 | P4 | ||
TMEM213 | ENST00000413208.1 | c.214G>A | p.Val72Met | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461462Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726982
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jun 20, 2021 | This sequence change replaces threonine with isoleucine at codon 1944 of the KIAA1549 protein (p.Thr1944Ile). The threonine residue is weakly conserved and there is a moderate physicochemical difference between threonine and isoleucine. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with KIAA1549-related conditions. This variant is not present in population databases (ExAC no frequency). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at