chr9-15457960-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001039697.2(SNAPC3):c.981G>C(p.Arg327Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000709 in 1,409,598 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039697.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNAPC3 | NM_001039697.2 | c.981G>C | p.Arg327Ser | missense_variant, splice_region_variant | 8/9 | ENST00000380821.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNAPC3 | ENST00000380821.8 | c.981G>C | p.Arg327Ser | missense_variant, splice_region_variant | 8/9 | 1 | NM_001039697.2 | P1 | |
SNAPC3 | ENST00000610884.4 | c.981G>C | p.Arg327Ser | missense_variant, splice_region_variant | 8/12 | 1 | P1 | ||
SNAPC3 | ENST00000467062.5 | c.981G>C | p.Arg327Ser | missense_variant, splice_region_variant, NMD_transcript_variant | 8/12 | 1 | |||
SNAPC3 | ENST00000490969.5 | c.981G>C | p.Arg327Ser | missense_variant, splice_region_variant, NMD_transcript_variant | 8/10 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000454 AC: 1AN: 220160Hom.: 0 AF XY: 0.00000836 AC XY: 1AN XY: 119602
GnomAD4 exome AF: 7.09e-7 AC: 1AN: 1409598Hom.: 0 Cov.: 26 AF XY: 0.00000142 AC XY: 1AN XY: 702048
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2022 | The c.981G>C (p.R327S) alteration is located in exon 8 (coding exon 8) of the SNAPC3 gene. This alteration results from a G to C substitution at nucleotide position 981, causing the arginine (R) at amino acid position 327 to be replaced by a serine (S). 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