7-138837988-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001164665.2(KIAA1549):c.5771C>T(p.Ser1924Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,240 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S1924S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164665.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA1549 | NM_001164665.2 | c.5771C>T | p.Ser1924Leu | missense_variant | 20/20 | ENST00000422774.2 | |
KIAA1549 | NM_020910.3 | c.5723C>T | p.Ser1908Leu | missense_variant | 20/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA1549 | ENST00000422774.2 | c.5771C>T | p.Ser1924Leu | missense_variant | 20/20 | 1 | NM_001164665.2 | A2 | |
KIAA1549 | ENST00000440172.5 | c.5723C>T | p.Ser1908Leu | missense_variant | 20/20 | 1 | P4 | ||
TMEM213 | ENST00000413208.1 | c.274G>A | p.Glu92Lys | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247474Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134238
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461006Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726666
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152234Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.5771C>T (p.S1924L) alteration is located in exon 20 (coding exon 20) of the KIAA1549 gene. This alteration results from a C to T substitution at nucleotide position 5771, causing the serine (S) at amino acid position 1924 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at