3-185598441-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021627.3(SENP2):c.187C>T(p.Leu63Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,774 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021627.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SENP2 | NM_021627.3 | c.187C>T | p.Leu63Phe | missense_variant | Exon 3 of 17 | ENST00000296257.10 | NP_067640.2 | |
SENP2 | XM_005247690.4 | c.187C>T | p.Leu63Phe | missense_variant | Exon 3 of 16 | XP_005247747.2 | ||
SENP2 | XM_005247691.4 | c.-125C>T | upstream_gene_variant | XP_005247748.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251336Hom.: 1 AF XY: 0.00 AC XY: 0AN XY: 135856
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461774Hom.: 1 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727196
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.187C>T (p.L63F) alteration is located in exon 3 (coding exon 3) of the SENP2 gene. This alteration results from a C to T substitution at nucleotide position 187, causing the leucine (L) at amino acid position 63 to be replaced by a phenylalanine (F). 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