chrX-115622196-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005032.7(PLS3):c.74-50C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00816 in 1,024,046 control chromosomes in the GnomAD database, including 372 homozygotes. There are 2,219 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.038 ( 209 hom., 1132 hem., cov: 23)
Exomes 𝑓: 0.0045 ( 163 hom. 1087 hem. )
Consequence
PLS3
NM_005032.7 intron
NM_005032.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.52
Genes affected
PLS3 (HGNC:9091): (plastin 3) 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. Plastin 1 (otherwise known as Fimbrin) is a third distinct plastin isoform which is specifically expressed at high levels in the small intestine. The L isoform is expressed only in hemopoietic cell lineages, while the T isoform has been found in all other normal cells of solid tissues that have replicative potential (fibroblasts, endothelial cells, epithelial cells, melanocytes, etc.). The C-terminal 570 amino acids of the T-plastin and L-plastin proteins are 83% identical. It contains a potential calcium-binding site near the N terminus. Alternate splicing results in multiple transcript variants.[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=-0.91).
BP6
?
Variant X-115622196-C-A is Benign according to our data. Variant chrX-115622196-C-A is described in ClinVar as [Benign]. Clinvar id is 1243943.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLS3 | NM_005032.7 | c.74-50C>A | intron_variant | ENST00000355899.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLS3 | ENST00000355899.8 | c.74-50C>A | intron_variant | 1 | NM_005032.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0380 AC: 4245AN: 111812Hom.: 209 Cov.: 23 AF XY: 0.0329 AC XY: 1120AN XY: 33992
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GnomAD3 exomes AF: 0.0121 AC: 1875AN: 155553Hom.: 87 AF XY: 0.00794 AC XY: 383AN XY: 48239
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GnomAD4 exome AF: 0.00449 AC: 4098AN: 912182Hom.: 163 Cov.: 14 AF XY: 0.00422 AC XY: 1087AN XY: 257328
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GnomAD4 genome ? AF: 0.0381 AC: 4260AN: 111864Hom.: 209 Cov.: 23 AF XY: 0.0332 AC XY: 1132AN XY: 34054
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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 | Jul 07, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at