X-115610487-CT-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_005032.7(PLS3):c.73+178del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00899 in 93,920 control chromosomes in the GnomAD database, including 6 homozygotes. There are 125 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0090 ( 6 hom., 125 hem., cov: 21)
Consequence
PLS3
NM_005032.7 intron
NM_005032.7 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.79
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 -10 ACMG points.
BP6
Variant X-115610487-CT-C is Benign according to our data. Variant chrX-115610487-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1186573.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00899 (844/93920) while in subpopulation AFR AF= 0.024 (629/26259). AF 95% confidence interval is 0.0224. There are 6 homozygotes in gnomad4. There are 125 alleles in male gnomad4 subpopulation. Median coverage is 21. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLS3 | NM_005032.7 | c.73+178del | intron_variant | ENST00000355899.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLS3 | ENST00000355899.8 | c.73+178del | intron_variant | 1 | NM_005032.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00900 AC: 845AN: 93930Hom.: 6 Cov.: 21 AF XY: 0.00508 AC XY: 125AN XY: 24600
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.00899 AC: 844AN: 93920Hom.: 6 Cov.: 21 AF XY: 0.00508 AC XY: 125AN XY: 24600
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 13, 2020 | - - |
Computational scores
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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