rs780412607
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001123385.2(BCOR):c.3950C>T(p.Pro1317Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000295 in 1,187,150 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P1317P) has been classified as Likely benign.
Frequency
Consequence
NM_001123385.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCOR | NM_001123385.2 | c.3950C>T | p.Pro1317Leu | missense_variant | 9/15 | ENST00000378444.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCOR | ENST00000378444.9 | c.3950C>T | p.Pro1317Leu | missense_variant | 9/15 | 1 | NM_001123385.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000268 AC: 3AN: 111984Hom.: 0 Cov.: 22 AF XY: 0.0000293 AC XY: 1AN XY: 34132
GnomAD3 exomes AF: 0.000128 AC: 18AN: 140429Hom.: 0 AF XY: 0.000139 AC XY: 6AN XY: 43257
GnomAD4 exome AF: 0.0000298 AC: 32AN: 1075115Hom.: 0 Cov.: 32 AF XY: 0.0000315 AC XY: 11AN XY: 349163
GnomAD4 genome ? AF: 0.0000268 AC: 3AN: 112035Hom.: 0 Cov.: 22 AF XY: 0.0000292 AC XY: 1AN XY: 34193
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The BCOR p.Pro1317Leu variant was not identified in the literature nor was it identified in Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs780412607) and ClinVar (classified as benign by Invitae for Oculofaciocardiodental syndrome). The variant was also identified in control databases in 18 of 140429 chromosomes (6 hemizygous) at a frequency of 0.000128 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the East Asian population in 18 of 10809 chromosomes (freq: 0.001665), but not in the African, Latino, Ashkenazi Jewish, European (Finnish), European (non-Finnish), Other or South Asian populations. The p.Pro1317 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and 3 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign. - |
Oculofaciocardiodental syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at