17-55078108-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178509.6(STXBP4):c.1219A>G(p.Met407Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,611,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178509.6 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 |
---|---|---|---|---|---|---|---|
STXBP4 | NM_178509.6 | c.1219A>G | p.Met407Val | missense_variant | 14/18 | ENST00000376352.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STXBP4 | ENST00000376352.6 | c.1219A>G | p.Met407Val | missense_variant | 14/18 | 2 | NM_178509.6 | P1 | |
STXBP4 | ENST00000434978.6 | c.1153A>G | p.Met385Val | missense_variant | 13/17 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248632Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134352
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1458842Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 725672
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 02, 2023 | The c.1219A>G (p.M407V) alteration is located in exon 14 (coding exon 12) of the STXBP4 gene. This alteration results from a A to G substitution at nucleotide position 1219, causing the methionine (M) at amino acid position 407 to be replaced by a valine (V). 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