rs144586803
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001048166.1(STIL):c.3067G>T(p.Val1023Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000663 in 1,613,822 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1023M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001048166.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STIL | NM_001048166.1 | c.3067G>T | p.Val1023Leu | missense_variant | 16/17 | ENST00000371877.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STIL | ENST00000371877.8 | c.3067G>T | p.Val1023Leu | missense_variant | 16/17 | 1 | NM_001048166.1 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.000309 AC: 47AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251108Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135756
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461544Hom.: 1 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 727020
GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74464
ClinVar
Submissions by phenotype
Microcephaly 7, primary, autosomal recessive Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 19, 2014 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at