rs958998
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032448.3(FAM120B):c.2284-350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,152 control chromosomes in the GnomAD database, including 47,616 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 0.79 ( 47616 hom., cov: 32)
Consequence
FAM120B
NM_032448.3 intron
NM_032448.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.111
Genes affected
FAM120B (HGNC:21109): (family with sequence similarity 120 member B) Predicted to be involved in fat cell differentiation and peroxisome proliferator activated receptor signaling pathway. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM120B | NM_032448.3 | c.2284-350A>G | intron_variant | ENST00000476287.4 | |||
LOC124901474 | XR_007059897.1 | n.137-358T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM120B | ENST00000476287.4 | c.2284-350A>G | intron_variant | 1 | NM_032448.3 | A2 | |||
FAM120B | ENST00000537664.5 | c.2353-350A>G | intron_variant | 2 | A2 | ||||
FAM120B | ENST00000625626.1 | c.280-350A>G | intron_variant | 2 | P2 | ||||
FAM120B | ENST00000630384.2 | c.2320-350A>G | intron_variant | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.790 AC: 120114AN: 152034Hom.: 47582 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: 0.790 AC: 120205AN: 152152Hom.: 47616 Cov.: 32 AF XY: 0.793 AC XY: 58989AN XY: 74388
GnomAD4 genome
?
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120205
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32
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58989
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74388
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3199
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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