6-35787903-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001010886.5(CLPSL1):c.259C>T(p.Arg87Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,606,962 control chromosomes in the GnomAD database, including 2 homozygotes. 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_001010886.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLPSL1 | NM_001010886.5 | c.259C>T | p.Arg87Trp | missense_variant | Exon 3 of 3 | ENST00000373861.6 | NP_001010886.1 | |
CLPSL1 | XM_017010820.2 | c.271C>T | p.Arg91Trp | missense_variant | Exon 2 of 2 | XP_016866309.1 | ||
CLPSL1 | NM_001348773.2 | c.222+783C>T | intron_variant | Intron 2 of 2 | NP_001335702.1 | |||
CLPSL1 | XM_017010821.2 | c.234+783C>T | intron_variant | Intron 1 of 1 | XP_016866310.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000144 AC: 22AN: 152258Hom.: 0 Cov.: 40
GnomAD3 exomes AF: 0.000232 AC: 58AN: 249550Hom.: 0 AF XY: 0.000295 AC XY: 40AN XY: 135398
GnomAD4 exome AF: 0.000180 AC: 262AN: 1454704Hom.: 2 Cov.: 32 AF XY: 0.000210 AC XY: 152AN XY: 724092
GnomAD4 genome AF: 0.000144 AC: 22AN: 152258Hom.: 0 Cov.: 40 AF XY: 0.000148 AC XY: 11AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.259C>T (p.R87W) alteration is located in exon 3 (coding exon 3) of the CLPSL1 gene. This alteration results from a C to T substitution at nucleotide position 259, causing the arginine (R) at amino acid position 87 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