chr12-111681753-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006768.5(BRAP):c.327A>C(p.Glu109Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,614,038 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006768.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAP | NM_006768.5 | c.327A>C | p.Glu109Asp | missense_variant | 3/12 | ENST00000419234.9 | |
BRAP | XM_005253944.5 | c.450A>C | p.Glu150Asp | missense_variant | 3/12 | ||
BRAP | XM_017019992.2 | c.165A>C | p.Glu55Asp | missense_variant | 2/11 | ||
BRAP | XM_047429622.1 | c.-5+1393A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAP | ENST00000419234.9 | c.327A>C | p.Glu109Asp | missense_variant | 3/12 | 1 | NM_006768.5 | P1 | |
BRAP | ENST00000327551.6 | c.237A>C | p.Glu79Asp | missense_variant | 3/12 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251464Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135906
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461842Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727216
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152196Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2022 | The c.327A>C (p.E109D) alteration is located in exon 3 (coding exon 3) of the BRAP gene. This alteration results from a A to C substitution at nucleotide position 327, causing the glutamic acid (E) at amino acid position 109 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at