rs2629540
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014661.4(FAM53B):c.-175+6434C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,096 control chromosomes in the GnomAD database, including 3,239 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.19 ( 3239 hom., cov: 32)
Consequence
FAM53B
NM_014661.4 intron
NM_014661.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0460
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM53B | NM_014661.4 | c.-175+6434C>G | intron_variant | ENST00000337318.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM53B | ENST00000337318.8 | c.-175+6434C>G | intron_variant | 1 | NM_014661.4 | P1 | |||
FAM53B | ENST00000280780.6 | c.-175+6434C>G | intron_variant | 1 | |||||
FAM53B | ENST00000392754.7 | c.-175+4849C>G | intron_variant | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.186 AC: 28205AN: 151976Hom.: 3236 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.185 AC: 28203AN: 152096Hom.: 3239 Cov.: 32 AF XY: 0.187 AC XY: 13930AN XY: 74336
GnomAD4 genome
?
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28203
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32
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13930
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74336
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531
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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