rs6094753
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_181659.3(NCOA3):c.823+2007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,944 control chromosomes in the GnomAD database, including 16,824 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 0.46 ( 16824 hom., cov: 32)
Consequence
NCOA3
NM_181659.3 intron
NM_181659.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.622
Genes affected
NCOA3 (HGNC:7670): (nuclear receptor coactivator 3) The protein encoded by this gene is a nuclear receptor coactivator that interacts with nuclear hormone receptors to enhance their transcriptional activator functions. The encoded protein has histone acetyltransferase activity and recruits p300/CBP-associated factor and CREB binding protein as part of a multisubunit coactivation complex. This protein is initially found in the cytoplasm but is translocated into the nucleus upon phosphorylation. Several transcript variants encoding different isoforms have been found for this gene. In addition, a polymorphic repeat region is found in the C-terminus of the encoded protein. [provided by RefSeq, Mar 2010]
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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 (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOA3 | NM_181659.3 | c.823+2007G>A | intron_variant | ENST00000371998.8 | |||
NCOA3 | NM_001174087.2 | c.823+2007G>A | intron_variant | ||||
NCOA3 | NM_001174088.2 | c.823+2007G>A | intron_variant | ||||
NCOA3 | NM_006534.4 | c.823+2007G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOA3 | ENST00000371998.8 | c.823+2007G>A | intron_variant | 1 | NM_181659.3 | P4 | |||
NCOA3 | ENST00000371997.3 | c.823+2007G>A | intron_variant | 1 | A2 | ||||
NCOA3 | ENST00000372004.7 | c.823+2007G>A | intron_variant | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.462 AC: 70181AN: 151826Hom.: 16798 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: 0.462 AC: 70253AN: 151944Hom.: 16824 Cov.: 32 AF XY: 0.454 AC XY: 33722AN XY: 74252
GnomAD4 genome
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74252
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1209
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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