chr10-10798774-T-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_ModerateBP6_ModerateBS2
The NM_001326327.2(CELF2):āc.10T>Gā(p.Leu4Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 398,898 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001326327.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CELF2 | NM_001326327.2 | c.10T>G | p.Leu4Val | missense_variant | 1/15 | ||
CELF2 | NM_001326326.2 | c.10T>G | p.Leu4Val | missense_variant | 1/15 | ||
CELF2 | XM_047424484.1 | c.10T>G | p.Leu4Val | missense_variant | 2/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CELF2 | ENST00000637215.1 | c.10T>G | p.Leu4Val | missense_variant | 1/15 | 5 | |||
CELF2 | ENST00000636488.1 | c.10T>G | p.Leu4Val | missense_variant | 1/14 | 5 | |||
CELF2 | ENST00000638035.1 | c.-193T>G | 5_prime_UTR_variant | 1/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152234Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000608 AC: 15AN: 246546Hom.: 0 Cov.: 0 AF XY: 0.0000480 AC XY: 6AN XY: 124968
GnomAD4 genome AF: 0.000223 AC: 34AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74504
ClinVar
Submissions by phenotype
CELF2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 21, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at