chr3-142683985-CT-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001145319.2(PLS1):c.580-11del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00597 in 1,143,190 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0060 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PLS1
NM_001145319.2 intron
NM_001145319.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.00700
Genes affected
PLS1 (HGNC:9090): (plastin 1) Plastins are a family of actin-binding proteins that are conserved throughout eukaryote evolution and expressed in most tissues of higher eukaryotes. In humans, two ubiquitous plastin isoforms (L and T) have been identified. The protein encoded by this gene is a third distinct plastin isoform, which is specifically expressed at high levels in the small intestine. Alternatively spliced transcript variants varying in the 5' UTR, but encoding the same protein, have been found for this gene. A pseudogene of this gene is found on chromosome 11.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant 3-142683985-CT-C is Benign according to our data. Variant chr3-142683985-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 3056069.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLS1 | NM_001145319.2 | c.580-11del | intron_variant | ENST00000457734.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLS1 | ENST00000457734.7 | c.580-11del | intron_variant | 2 | NM_001145319.2 | P1 | |||
ENST00000690164.1 | n.119-26780del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 10AN: 147470Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome AF: 0.00597 AC: 6830AN: 1143190Hom.: 0 Cov.: 27 AF XY: 0.00626 AC XY: 3542AN XY: 566168
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000678 AC: 10AN: 147540Hom.: 0 Cov.: 32 AF XY: 0.0000557 AC XY: 4AN XY: 71818
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PLS1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 14, 2020 | 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). - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at