3-94014846-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001850.3(STX19):c.424C>T(p.Arg142Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,613,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX19 | NM_001001850.3 | c.424C>T | p.Arg142Cys | missense_variant | 2/2 | ENST00000315099.3 | |
ARL13B | NM_001174150.2 | c.380+10938G>A | intron_variant | ENST00000394222.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX19 | ENST00000315099.3 | c.424C>T | p.Arg142Cys | missense_variant | 2/2 | 1 | NM_001001850.3 | P1 | |
ARL13B | ENST00000394222.8 | c.380+10938G>A | intron_variant | 1 | NM_001174150.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152100Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000251 AC: 63AN: 250706Hom.: 0 AF XY: 0.000251 AC XY: 34AN XY: 135484
GnomAD4 exome AF: 0.000129 AC: 188AN: 1461780Hom.: 0 Cov.: 32 AF XY: 0.000133 AC XY: 97AN XY: 727180
GnomAD4 genome AF: 0.0000855 AC: 13AN: 152100Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.424C>T (p.R142C) alteration is located in exon 2 (coding exon 1) of the STX19 gene. This alteration results from a C to T substitution at nucleotide position 424, causing the arginine (R) at amino acid position 142 to be replaced by a cysteine (C). 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