chr22-20859121-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004782.4(SNAP29):c.11A>G(p.Tyr4Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,606,626 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. Y4Y) has been classified as Likely benign.
Frequency
Consequence
NM_004782.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNAP29 | NM_004782.4 | c.11A>G | p.Tyr4Cys | missense_variant | 1/5 | ENST00000215730.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAP29 | ENST00000215730.12 | c.11A>G | p.Tyr4Cys | missense_variant | 1/5 | 1 | NM_004782.4 | P1 | |
PI4KA | ENST00000449120.1 | c.-19+2T>C | splice_donor_variant | 4 | |||||
SNAP29 | ENST00000490458.1 | n.41A>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152040Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000876 AC: 2AN: 228258Hom.: 0 AF XY: 0.00000799 AC XY: 1AN XY: 125192
GnomAD4 exome AF: 0.0000124 AC: 18AN: 1454586Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 723198
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152040Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74272
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.11A>G (p.Y4C) alteration is located in exon 1 (coding exon 1) of the SNAP29 gene. This alteration results from a A to G substitution at nucleotide position 11, causing the tyrosine (Y) at amino acid position 4 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