20-63642257-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015894.4(STMN3):c.334G>A(p.Glu112Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000226 in 1,545,716 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015894.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STMN3 | NM_015894.4 | c.334G>A | p.Glu112Lys | missense_variant | Exon 4 of 5 | ENST00000370053.3 | NP_056978.2 | |
STMN3 | NM_001276310.2 | c.301G>A | p.Glu101Lys | missense_variant | Exon 4 of 5 | NP_001263239.1 | ||
STMN3 | NR_075070.2 | n.510G>A | non_coding_transcript_exon_variant | Exon 4 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STMN3 | ENST00000370053.3 | c.334G>A | p.Glu112Lys | missense_variant | Exon 4 of 5 | 1 | NM_015894.4 | ENSP00000359070.1 | ||
STMN3 | ENST00000631920.1 | c.508G>A | p.Glu170Lys | missense_variant | Exon 4 of 5 | 2 | ENSP00000487795.1 | |||
STMN3 | ENST00000540534.5 | c.301G>A | p.Glu101Lys | missense_variant | Exon 4 of 5 | 2 | ENSP00000439840.1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151670Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000466 AC: 9AN: 193334Hom.: 0 AF XY: 0.0000557 AC XY: 6AN XY: 107798
GnomAD4 exome AF: 0.0000230 AC: 32AN: 1394046Hom.: 0 Cov.: 35 AF XY: 0.0000231 AC XY: 16AN XY: 693420
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151670Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2AN XY: 74056
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.334G>A (p.E112K) alteration is located in exon 4 (coding exon 4) of the STMN3 gene. This alteration results from a G to A substitution at nucleotide position 334, causing the glutamic acid (E) at amino acid position 112 to be replaced by a lysine (K). 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