1-35736990-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_022111.4(CLSPN):c.3833G>A(p.Arg1278Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_022111.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLSPN | NM_022111.4 | c.3833G>A | p.Arg1278Gln | missense_variant | Exon 24 of 25 | ENST00000318121.8 | NP_071394.2 | |
CLSPN | NM_001330490.2 | c.3833G>A | p.Arg1278Gln | missense_variant | Exon 24 of 25 | NP_001317419.1 | ||
CLSPN | NM_001190481.2 | c.3641G>A | p.Arg1214Gln | missense_variant | Exon 23 of 24 | NP_001177410.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251410Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135872
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461856Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727232
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3833G>A (p.R1278Q) alteration is located in exon 24 (coding exon 24) of the CLSPN gene. This alteration results from a G to A substitution at nucleotide position 3833, causing the arginine (R) at amino acid position 1278 to be replaced by a glutamine (Q). 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