chrX-16757300-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032796.4(SYAP1):c.922G>A(p.Val308Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000317 in 1,198,964 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032796.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYAP1 | NM_032796.4 | c.922G>A | p.Val308Ile | missense_variant | 8/9 | ENST00000380155.4 | |
SYAP1 | NR_033181.2 | n.997G>A | non_coding_transcript_exon_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYAP1 | ENST00000380155.4 | c.922G>A | p.Val308Ile | missense_variant | 8/9 | 1 | NM_032796.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000717 AC: 8AN: 111532Hom.: 0 Cov.: 22 AF XY: 0.000119 AC XY: 4AN XY: 33712
GnomAD3 exomes AF: 0.0000798 AC: 14AN: 175420Hom.: 0 AF XY: 0.0000326 AC XY: 2AN XY: 61356
GnomAD4 exome AF: 0.0000276 AC: 30AN: 1087378Hom.: 0 Cov.: 29 AF XY: 0.0000197 AC XY: 7AN XY: 354438
GnomAD4 genome AF: 0.0000717 AC: 8AN: 111586Hom.: 0 Cov.: 22 AF XY: 0.000118 AC XY: 4AN XY: 33776
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.922G>A (p.V308I) alteration is located in exon 8 (coding exon 8) of the SYAP1 gene. This alteration results from a G to A substitution at nucleotide position 922, causing the valine (V) at amino acid position 308 to be replaced by an isoleucine (I). 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