chr10-124682144-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014661.4(FAM53B):c.369G>A(p.Met123Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000892 in 1,613,490 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 0.000072 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000091 ( 0 hom. )
Consequence
FAM53B
NM_014661.4 missense
NM_014661.4 missense
Scores
1
5
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.08
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.02833876).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM53B | NM_014661.4 | c.369G>A | p.Met123Ile | missense_variant | 4/5 | ENST00000337318.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM53B | ENST00000337318.8 | c.369G>A | p.Met123Ile | missense_variant | 4/5 | 1 | NM_014661.4 | P1 | |
FAM53B | ENST00000280780.6 | c.369G>A | p.Met123Ile | missense_variant | 4/5 | 1 | |||
FAM53B | ENST00000392754.7 | c.369G>A | p.Met123Ile | missense_variant | 4/5 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152200Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000217 AC: 54AN: 249304Hom.: 0 AF XY: 0.000215 AC XY: 29AN XY: 135052
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GnomAD4 exome AF: 0.0000910 AC: 133AN: 1461290Hom.: 0 Cov.: 32 AF XY: 0.0000784 AC XY: 57AN XY: 726940
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GnomAD4 genome AF: 0.0000723 AC: 11AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74362
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
D;D;D
Sift4G
Uncertain
T;T;D
Polyphen
B;B;B
Vest4
MutPred
Loss of phosphorylation at T128 (P = 0.0969);Loss of phosphorylation at T128 (P = 0.0969);Loss of phosphorylation at T128 (P = 0.0969);
MVP
MPC
ClinPred
T
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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