rs7851693
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003934.2(FUBP3):c.191-6514C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000066 in 151,516 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 30)
Consequence
FUBP3
NM_003934.2 intron
NM_003934.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.694
Genes affected
FUBP3 (HGNC:4005): (far upstream element binding protein 3) Enables single-stranded DNA binding activity. Involved in positive regulation of gene expression; positive regulation of transcription, DNA-templated; and transcription, DNA-templated. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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 (BayesDel_noAF=-0.88).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUBP3 | NM_003934.2 | c.191-6514C>A | intron_variant | ENST00000319725.10 | |||
FUBP3 | XM_005272232.3 | c.191-6514C>A | intron_variant | ||||
FUBP3 | XM_011519172.4 | c.191-6514C>A | intron_variant | ||||
FUBP3 | XR_007061369.1 | n.295-6514C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUBP3 | ENST00000319725.10 | c.191-6514C>A | intron_variant | 1 | NM_003934.2 | P1 | |||
FUBP3 | ENST00000650723.1 | c.*911-3858C>A | intron_variant, NMD_transcript_variant | ||||||
FUBP3 | ENST00000699747.1 | c.*79-6517C>A | intron_variant, NMD_transcript_variant | ||||||
FUBP3 | ENST00000465949.1 | n.526-6514C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151516Hom.: 0 Cov.: 30
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GnomAD4 genome ? AF: 0.00000660 AC: 1AN: 151516Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 73936
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ClinVar
Not reported inComputational scores
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Name
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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