14-99174183-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_138576.4(BCL11B):c.2653G>A(p.Asp885Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,246 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 Uncertain significance (★★).
Frequency
Consequence
NM_138576.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCL11B | ENST00000357195.8 | c.2653G>A | p.Asp885Asn | missense_variant | Exon 4 of 4 | 1 | NM_138576.4 | ENSP00000349723.3 | ||
BCL11B | ENST00000345514.2 | c.2440G>A | p.Asp814Asn | missense_variant | Exon 3 of 3 | 1 | ENSP00000280435.6 | |||
BCL11B | ENST00000443726.2 | c.2071G>A | p.Asp691Asn | missense_variant | Exon 2 of 2 | 5 | ENSP00000387419.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461246Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726962
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:2
BCL11B: PM2, PP2 -
This variant is not present in population databases (ExAC no frequency). This sequence change replaces aspartic acid with asparagine at codon 885 of the BCL11B protein (p.Asp885Asn). The aspartic acid residue is highly conserved and there is a small physicochemical difference between aspartic acid and asparagine. This variant has not been reported in the literature in individuals with BCL11B-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.