chr2-121367677-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBS1BS2
The NM_001395891.1(CLASP1):c.3860C>T(p.Pro1287Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000898 in 1,614,038 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P1287P) has been classified as Likely benign.
Frequency
Consequence
NM_001395891.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLASP1 | NM_001395891.1 | c.3860C>T | p.Pro1287Leu | missense_variant | 36/41 | ENST00000696935.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLASP1 | ENST00000696935.1 | c.3860C>T | p.Pro1287Leu | missense_variant | 36/41 | NM_001395891.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000317 AC: 79AN: 249300Hom.: 1 AF XY: 0.000259 AC XY: 35AN XY: 135250
GnomAD4 exome AF: 0.0000794 AC: 116AN: 1461712Hom.: 1 Cov.: 32 AF XY: 0.0000646 AC XY: 47AN XY: 727138
GnomAD4 genome ? AF: 0.000190 AC: 29AN: 152326Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74470
ClinVar
Submissions by phenotype
CLASP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 28, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at