19-55306276-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_032430.2(BRSK1):c.1915C>G(p.Leu639Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,614,076 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_032430.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRSK1 | NM_032430.2 | c.1915C>G | p.Leu639Val | missense_variant | 17/19 | ENST00000309383.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRSK1 | ENST00000309383.6 | c.1915C>G | p.Leu639Val | missense_variant | 17/19 | 1 | NM_032430.2 | P1 | |
BRSK1 | ENST00000590333.5 | c.1963C>G | p.Leu655Val | missense_variant | 19/21 | 1 | |||
BRSK1 | ENST00000326848.7 | c.1000C>G | p.Leu334Val | missense_variant | 9/11 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251254Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135856
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461730Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727192
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 09, 2023 | The c.1915C>G (p.L639V) alteration is located in exon 17 (coding exon 17) of the BRSK1 gene. This alteration results from a C to G substitution at nucleotide position 1915, causing the leucine (L) at amino acid position 639 to be replaced by a valine (V). 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