chr2-240998935-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001080437.3(SNED1):āc.98C>Gā(p.Pro33Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000156 in 1,279,590 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001080437.3 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SNED1 | NM_001080437.3 | c.98C>G | p.Pro33Arg | missense_variant | 1/32 | ENST00000310397.13 | NP_001073906.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SNED1 | ENST00000310397.13 | c.98C>G | p.Pro33Arg | missense_variant | 1/32 | 5 | NM_001080437.3 | ENSP00000308893.8 | ||
SNED1 | ENST00000405547.7 | c.98C>G | p.Pro33Arg | missense_variant | 1/30 | 5 | ENSP00000386007.3 | |||
SNED1 | ENST00000401884.5 | c.98C>G | p.Pro33Arg | missense_variant | 1/27 | 5 | ENSP00000384871.1 |
Frequencies
GnomAD3 genomes AF: 0.00000667 AC: 1AN: 150006Hom.: 0 Cov.: 32
GnomAD4 exome AF: 8.85e-7 AC: 1AN: 1129584Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 546404
GnomAD4 genome AF: 0.00000667 AC: 1AN: 150006Hom.: 0 Cov.: 32 AF XY: 0.0000137 AC XY: 1AN XY: 73192
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 08, 2024 | The c.98C>G (p.P33R) alteration is located in exon 1 (coding exon 1) of the SNED1 gene. This alteration results from a C to G substitution at nucleotide position 98, causing the proline (P) at amino acid position 33 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