chr3-142676111-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001145319.2(PLS1):c.365-46A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00799 in 1,566,386 control chromosomes in the GnomAD database, including 832 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.043 ( 443 hom., cov: 32)
Exomes 𝑓: 0.0043 ( 389 hom. )
Consequence
PLS1
NM_001145319.2 intron
NM_001145319.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0910
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 3-142676111-A-G is Benign according to our data. Variant chr3-142676111-A-G is described in ClinVar as [Benign]. Clinvar id is 1239682.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLS1 | NM_001145319.2 | c.365-46A>G | intron_variant | ENST00000457734.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLS1 | ENST00000457734.7 | c.365-46A>G | intron_variant | 2 | NM_001145319.2 | P1 | |||
ENST00000690164.1 | n.119-18905T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0426 AC: 6480AN: 152214Hom.: 439 Cov.: 32
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GnomAD3 exomes AF: 0.0114 AC: 2641AN: 231174Hom.: 181 AF XY: 0.00842 AC XY: 1057AN XY: 125464
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GnomAD4 exome AF: 0.00426 AC: 6021AN: 1414054Hom.: 389 Cov.: 26 AF XY: 0.00366 AC XY: 2580AN XY: 705466
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GnomAD4 genome ? AF: 0.0427 AC: 6502AN: 152332Hom.: 443 Cov.: 32 AF XY: 0.0416 AC XY: 3099AN XY: 74506
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 22, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at