chr3-94015069-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001001850.3(STX19):c.201T>A(p.Asn67Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000231 in 1,613,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001001850.3 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 |
---|---|---|---|---|---|---|---|
STX19 | NM_001001850.3 | c.201T>A | p.Asn67Lys | missense_variant | 2/2 | ENST00000315099.3 | |
ARL13B | NM_001174150.2 | c.380+11161A>T | intron_variant | ENST00000394222.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX19 | ENST00000315099.3 | c.201T>A | p.Asn67Lys | missense_variant | 2/2 | 1 | NM_001001850.3 | P1 | |
ARL13B | ENST00000394222.8 | c.380+11161A>T | intron_variant | 1 | NM_001174150.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000116 AC: 29AN: 250916Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135676
GnomAD4 exome AF: 0.000239 AC: 350AN: 1461630Hom.: 0 Cov.: 32 AF XY: 0.000245 AC XY: 178AN XY: 727116
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152158Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 05, 2022 | The c.201T>A (p.N67K) alteration is located in exon 2 (coding exon 1) of the STX19 gene. This alteration results from a T to A substitution at nucleotide position 201, causing the asparagine (N) at amino acid position 67 to be replaced by a lysine (K). 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