5-170258159-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The ENST00000046794.10(LCP2):c.978G>A(p.Gln326=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 1,612,780 control chromosomes in the GnomAD database, including 194,689 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.53 ( 22216 hom., cov: 32)
Exomes 𝑓: 0.48 ( 172473 hom. )
Consequence
LCP2
ENST00000046794.10 synonymous
ENST00000046794.10 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.30
Genes affected
LCP2 (HGNC:6529): (lymphocyte cytosolic protein 2) This gene encodes an adapter protein that acts as a substrate of the T cell antigen receptor (TCR)-activated protein tyrosine kinase pathway. The encoded protein associates with growth factor receptor bound protein 2, and is thought to play a role TCR-mediated intracellular signal transduction. A similar protein in mouse plays a role in normal T-cell development and activation. Mice lacking this gene show subcutaneous and intraperitoneal fetal hemorrhaging, dysfunctional platelets and impaired viability. [provided by RefSeq, Nov 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 5-170258159-C-T is Benign according to our data. Variant chr5-170258159-C-T is described in ClinVar as [Benign]. Clinvar id is 2687970.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-3.3 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LCP2 | NM_005565.5 | c.978G>A | p.Gln326= | synonymous_variant | 16/21 | ENST00000046794.10 | NP_005556.1 | |
LCP2 | XM_047417171.1 | c.747G>A | p.Gln249= | synonymous_variant | 14/19 | XP_047273127.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LCP2 | ENST00000046794.10 | c.978G>A | p.Gln326= | synonymous_variant | 16/21 | 1 | NM_005565.5 | ENSP00000046794 | P1 | |
LCP2 | ENST00000521416.5 | c.363G>A | p.Gln121= | synonymous_variant | 8/13 | 2 | ENSP00000428871 | |||
LCP2 | ENST00000520344.1 | c.279G>A | p.Gln93= | synonymous_variant | 7/8 | 5 | ENSP00000430391 | |||
LCP2 | ENST00000523369.1 | n.340G>A | non_coding_transcript_exon_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.534 AC: 81183AN: 151900Hom.: 22201 Cov.: 32
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GnomAD3 exomes AF: 0.510 AC: 126939AN: 249090Hom.: 32892 AF XY: 0.505 AC XY: 68277AN XY: 135162
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GnomAD4 exome AF: 0.484 AC: 706667AN: 1460762Hom.: 172473 Cov.: 40 AF XY: 0.483 AC XY: 350982AN XY: 726756
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GnomAD4 genome AF: 0.534 AC: 81239AN: 152018Hom.: 22216 Cov.: 32 AF XY: 0.540 AC XY: 40118AN XY: 74310
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Jan 24, 2024 | This variant is classified as Benign based on local population frequency. This variant was detected in 84% of patients studied by a panel of primary immunodeficiencies. Number of patients: 80. Only high quality variants are reported. - |
Computational scores
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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