10-10940683-C-T
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000428520.7(LINC00710):n.687+3500G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,978 control chromosomes in the GnomAD database, including 10,042 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000428520.7 intron
Scores
Clinical Significance
Conservation
Publications
- developmental and epileptic encephalopathy 97Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- undetermined early-onset epileptic encephalopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- complex neurodevelopmental disorderInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CELF2 | NM_001326325.2 | c.146+20684C>T | intron_variant | Intron 3 of 15 | NP_001313254.1 | |||
CELF2 | NM_001326327.2 | c.89+20684C>T | intron_variant | Intron 2 of 14 | NP_001313256.1 | |||
CELF2 | NM_001326326.2 | c.89+20684C>T | intron_variant | Intron 2 of 14 | NP_001313255.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINC00710 | ENST00000428520.7 | n.687+3500G>A | intron_variant | Intron 5 of 5 | 1 | |||||
LINC00710 | ENST00000635670.2 | n.455+3500G>A | intron_variant | Intron 3 of 4 | 1 | |||||
CELF2 | ENST00000637215.1 | c.89+20684C>T | intron_variant | Intron 2 of 14 | 5 | ENSP00000490185.1 |
Frequencies
GnomAD3 genomes AF: 0.346 AC: 52577AN: 151862Hom.: 10030 Cov.: 32 show subpopulations
GnomAD4 genome AF: 0.346 AC: 52628AN: 151978Hom.: 10042 Cov.: 32 AF XY: 0.359 AC XY: 26681AN XY: 74296 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at