3-185598522-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_021627.3(SENP2):c.268C>T(p.Arg90Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,858 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_021627.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SENP2 | NM_021627.3 | c.268C>T | p.Arg90Trp | missense_variant | Exon 3 of 17 | ENST00000296257.10 | NP_067640.2 | |
SENP2 | XM_005247691.4 | c.-44C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 15 | XP_005247748.1 | |||
SENP2 | XM_005247690.4 | c.268C>T | p.Arg90Trp | missense_variant | Exon 3 of 16 | XP_005247747.2 | ||
SENP2 | XM_005247691.4 | c.-44C>T | 5_prime_UTR_variant | Exon 1 of 15 | XP_005247748.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151998Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251364Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135838
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727232
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151998Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74216
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.268C>T (p.R90W) 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 268, causing the arginine (R) at amino acid position 90 to be replaced by a tryptophan (W). 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