rs374506776
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_153252.5(BRWD3):c.4398-7C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,172,066 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153252.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRWD3 | NM_153252.5 | c.4398-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000373275.5 | |||
BRWD3 | XM_005262113.4 | c.4248-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
BRWD3 | XM_017029384.2 | c.3186-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRWD3 | ENST00000373275.5 | c.4398-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_153252.5 | P1 | |||
BRWD3 | ENST00000473691.1 | n.2454-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000832 AC: 9AN: 108231Hom.: 0 Cov.: 22 AF XY: 0.0000651 AC XY: 2AN XY: 30713
GnomAD3 exomes AF: 0.0000441 AC: 8AN: 181284Hom.: 0 AF XY: 0.0000151 AC XY: 1AN XY: 66268
GnomAD4 exome AF: 0.0000141 AC: 15AN: 1063835Hom.: 0 Cov.: 27 AF XY: 0.00000601 AC XY: 2AN XY: 332693
GnomAD4 genome AF: 0.0000832 AC: 9AN: 108231Hom.: 0 Cov.: 22 AF XY: 0.0000651 AC XY: 2AN XY: 30713
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 18, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at