1-32381264-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018045.8(BSDC1):c.362G>A(p.Arg121His) variant causes a missense change. The variant allele was found at a frequency of 0.000041 in 1,609,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000039 ( 0 hom. )
Consequence
BSDC1
NM_018045.8 missense
NM_018045.8 missense
Scores
5
7
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.82
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.33013123).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BSDC1 | NM_018045.8 | c.362G>A | p.Arg121His | missense_variant | 5/11 | ENST00000455895.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BSDC1 | ENST00000455895.7 | c.362G>A | p.Arg121His | missense_variant | 5/11 | 1 | NM_018045.8 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152120Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000656 AC: 16AN: 243732Hom.: 0 AF XY: 0.0000604 AC XY: 8AN XY: 132366
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GnomAD4 exome AF: 0.0000391 AC: 57AN: 1457560Hom.: 0 Cov.: 30 AF XY: 0.0000469 AC XY: 34AN XY: 724866
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GnomAD4 genome AF: 0.0000591 AC: 9AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74432
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.;.;.;.;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.;.;.;.
MutationTaster
Benign
D;D;D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;N;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;D;D;T
Sift4G
Pathogenic
D;D;D;D;D;.;D
Polyphen
P;P;P;P;P;.;.
Vest4
MVP
MPC
0.53
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at