16-2209405-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_182563.4(BRICD5):c.644G>A(p.Ser215Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,613,818 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S215C) has been classified as Uncertain significance.
Frequency
Consequence
NM_182563.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRICD5 | ENST00000328540.8 | c.644G>A | p.Ser215Asn | missense_variant | Exon 6 of 6 | 1 | NM_182563.4 | ENSP00000332389.3 | ||
MLST8 | ENST00000569417.6 | c.*528C>T | 3_prime_UTR_variant | Exon 9 of 9 | 1 | NM_022372.6 | ENSP00000456405.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152198Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251042Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135800
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461502Hom.: 0 Cov.: 33 AF XY: 0.0000206 AC XY: 15AN XY: 727070
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152316Hom.: 0 Cov.: 34 AF XY: 0.0000940 AC XY: 7AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.644G>A (p.S215N) alteration is located in exon 6 (coding exon 6) of the BRICD5 gene. This alteration results from a G to A substitution at nucleotide position 644, causing the serine (S) at amino acid position 215 to be replaced by an asparagine (N). 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