rs778220343
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS2_Supporting
The NM_001379451.1(BCORL1):āc.532A>Gā(p.Thr178Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,209,900 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001379451.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCORL1 | NM_001379451.1 | c.532A>G | p.Thr178Ala | missense_variant | 4/14 | ENST00000540052.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCORL1 | ENST00000540052.6 | c.532A>G | p.Thr178Ala | missense_variant | 4/14 | 1 | NM_001379451.1 | P1 | |
BCORL1 | ENST00000218147.11 | c.532A>G | p.Thr178Ala | missense_variant | 4/13 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000358 AC: 4AN: 111680Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33886
GnomAD3 exomes AF: 0.0000218 AC: 4AN: 183444Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67886
GnomAD4 exome AF: 0.0000209 AC: 23AN: 1098220Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 8AN XY: 363584
GnomAD4 genome ? AF: 0.0000358 AC: 4AN: 111680Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33886
ClinVar
Submissions by phenotype
Autism;C0025990:Micrognathia;C0028738:Nystagmus;C0038273:Stereotypic movement disorder;C0264611:Speech apraxia;C0344482:Hypoplasia of the corpus callosum;C0423110:Downslanted palpebral fissures;C0454644:Delayed speech and language development;C0557874:Global developmental delay;C0856975:Autistic behavior;C0857379:Abnormal pinna morphology;C0948163:Abnormal cerebral white matter morphology;C1827524:Wide intermamillary distance;C1842581:Abnormal corpus callosum morphology;C1845251:Facial hypotonia;C1858091:Long fingers;C1858120:Generalized hypotonia;C1865572:Proximal placement of thumb;C1866195:Downturned corners of mouth;C2237142:Moderate global developmental delay;C3150613:Long toe;C4022908:Cerebral white matter hypoplasia;C4551563:Microcephaly Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Personalized Medicine, Children's Hospital Los Angeles | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at