12-111644317-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006768.5(BRAP):c.1661G>A(p.Arg554Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,898 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRAP | ENST00000419234.9 | c.1661G>A | p.Arg554Gln | missense_variant | Exon 12 of 12 | 1 | NM_006768.5 | ENSP00000403524.3 | ||
BRAP | ENST00000327551.6 | c.1571G>A | p.Arg524Gln | missense_variant | Exon 12 of 12 | 1 | ENSP00000330813.5 | |||
BRAP | ENST00000547043.1 | n.*22G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251442Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135896
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461872Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727238
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152026Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74220
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1661G>A (p.R554Q) alteration is located in exon 12 (coding exon 12) of the BRAP gene. This alteration results from a G to A substitution at nucleotide position 1661, causing the arginine (R) at amino acid position 554 to be replaced by a glutamine (Q). 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