rs112439044
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_014223.5(NFYC):c.387+1159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000801 in 534,396 control chromosomes in the GnomAD database, including 5 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 0.00049 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00093 ( 4 hom. )
Consequence
NFYC
NM_014223.5 intron
NM_014223.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.618
Genes affected
NFYC (HGNC:7806): (nuclear transcription factor Y subunit gamma) This gene encodes one subunit of a trimeric complex forming a highly conserved transcription factor that binds with high specificity to CCAAT motifs in the promoters of a variety of genes. The encoded protein, subunit C, forms a tight dimer with the B subunit, a prerequisite for subunit A association. The resulting trimer binds to DNA with high specificity and affinity. Subunits B and C each contain a histone-like motif. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BS2
High AC in GnomAd4 at 74 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NFYC | NM_014223.5 | c.387+1159C>T | intron_variant | ENST00000447388.8 | NP_055038.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NFYC | ENST00000447388.8 | c.387+1159C>T | intron_variant | 1 | NM_014223.5 | ENSP00000404427.3 |
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 74AN: 152138Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.00125 AC: 314AN: 250978Hom.: 3 AF XY: 0.00122 AC XY: 166AN XY: 135866
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GnomAD4 exome AF: 0.000926 AC: 354AN: 382140Hom.: 4 Cov.: 0 AF XY: 0.00102 AC XY: 221AN XY: 217576
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GnomAD4 genome AF: 0.000486 AC: 74AN: 152256Hom.: 1 Cov.: 31 AF XY: 0.000511 AC XY: 38AN XY: 74436
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at