rs35490896
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022111.4(CLSPN):c.3839C>T(p.Ser1280Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 1,613,982 control chromosomes in the GnomAD database, including 3,175 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_022111.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLSPN | NM_022111.4 | c.3839C>T | p.Ser1280Leu | missense_variant | 24/25 | ENST00000318121.8 | |
CLSPN | NM_001330490.2 | c.3839C>T | p.Ser1280Leu | missense_variant | 24/25 | ||
CLSPN | NM_001190481.2 | c.3647C>T | p.Ser1216Leu | missense_variant | 23/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLSPN | ENST00000318121.8 | c.3839C>T | p.Ser1280Leu | missense_variant | 24/25 | 1 | NM_022111.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0642 AC: 9764AN: 152118Hom.: 369 Cov.: 32
GnomAD3 exomes AF: 0.0553 AC: 13892AN: 251364Hom.: 443 AF XY: 0.0567 AC XY: 7697AN XY: 135848
GnomAD4 exome AF: 0.0595 AC: 87005AN: 1461746Hom.: 2807 Cov.: 31 AF XY: 0.0600 AC XY: 43646AN XY: 727166
GnomAD4 genome ? AF: 0.0643 AC: 9782AN: 152236Hom.: 368 Cov.: 32 AF XY: 0.0634 AC XY: 4723AN XY: 74438
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at