chr9-15423096-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039697.2(SNAPC3):c.217G>C(p.Gly73Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000368 in 1,542,636 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039697.2 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 |
---|---|---|---|---|---|---|---|
SNAPC3 | NM_001039697.2 | c.217G>C | p.Gly73Arg | missense_variant | 1/9 | ENST00000380821.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAPC3 | ENST00000380821.8 | c.217G>C | p.Gly73Arg | missense_variant | 1/9 | 1 | NM_001039697.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000167 AC: 28AN: 167374Hom.: 0 AF XY: 0.000202 AC XY: 19AN XY: 93958
GnomAD4 exome AF: 0.000383 AC: 532AN: 1390296Hom.: 0 Cov.: 31 AF XY: 0.000381 AC XY: 263AN XY: 689860
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 18, 2021 | The c.217G>C (p.G73R) alteration is located in exon 1 (coding exon 1) of the SNAPC3 gene. This alteration results from a G to C substitution at nucleotide position 217, causing the glycine (G) at amino acid position 73 to be replaced by an arginine (R). 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