chr10-10919970-G-A
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The ENST00000666257.1(LINC00710):n.1728-2016C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,231,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
LINC00710
ENST00000666257.1 intron, non_coding_transcript
ENST00000666257.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00500
Genes affected
LINC00710 (HGNC:27386): (long intergenic non-protein coding RNA 710)
CELF2 (HGNC:2550): (CUGBP Elav-like family member 2) Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BP6
Variant 10-10919970-G-A is Benign according to our data. Variant chr10-10919970-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2640298.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CELF2 | NM_001326325.2 | c.117G>A | p.Thr39= | synonymous_variant | 3/16 | ||
CELF2 | NM_001326327.2 | c.60G>A | p.Thr20= | synonymous_variant | 2/15 | ||
CELF2 | NM_001326326.2 | c.60G>A | p.Thr20= | synonymous_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC00710 | ENST00000666257.1 | n.1728-2016C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152108Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000128 AC: 138AN: 1079240Hom.: 0 Cov.: 29 AF XY: 0.000106 AC XY: 54AN XY: 509448
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GnomAD4 genome AF: 0.000138 AC: 21AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74420
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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 | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | CELF2: BP4, BP7 - |
Computational scores
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Benign
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Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at