rs2076546
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_181659.3(NCOA3):āc.2880A>Gā(p.Thr960=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0898 in 1,614,030 control chromosomes in the GnomAD database, including 7,859 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: š 0.13 ( 1711 hom., cov: 32)
Exomes š: 0.086 ( 6148 hom. )
Consequence
NCOA3
NM_181659.3 synonymous
NM_181659.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.947
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP7
?
Synonymous conserved (PhyloP=-0.947 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOA3 | NM_181659.3 | c.2880A>G | p.Thr960= | synonymous_variant | 15/23 | ENST00000371998.8 | |
NCOA3 | NM_001174087.2 | c.2880A>G | p.Thr960= | synonymous_variant | 15/23 | ||
NCOA3 | NM_006534.4 | c.2880A>G | p.Thr960= | synonymous_variant | 15/23 | ||
NCOA3 | NM_001174088.2 | c.2865A>G | p.Thr955= | synonymous_variant | 15/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOA3 | ENST00000371998.8 | c.2880A>G | p.Thr960= | synonymous_variant | 15/23 | 1 | NM_181659.3 | P4 | |
NCOA3 | ENST00000372004.7 | c.2880A>G | p.Thr960= | synonymous_variant | 15/23 | 1 | A2 | ||
NCOA3 | ENST00000371997.3 | c.2865A>G | p.Thr955= | synonymous_variant | 15/23 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.128 AC: 19404AN: 152044Hom.: 1706 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
19404
AN:
152044
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0925 AC: 23247AN: 251344Hom.: 1306 AF XY: 0.0921 AC XY: 12509AN XY: 135884
GnomAD3 exomes
AF:
AC:
23247
AN:
251344
Hom.:
AF XY:
AC XY:
12509
AN XY:
135884
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0859 AC: 125583AN: 1461868Hom.: 6148 Cov.: 33 AF XY: 0.0871 AC XY: 63323AN XY: 727234
GnomAD4 exome
AF:
AC:
125583
AN:
1461868
Hom.:
Cov.:
33
AF XY:
AC XY:
63323
AN XY:
727234
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.128 AC: 19421AN: 152162Hom.: 1711 Cov.: 32 AF XY: 0.125 AC XY: 9290AN XY: 74400
GnomAD4 genome
?
AF:
AC:
19421
AN:
152162
Hom.:
Cov.:
32
AF XY:
AC XY:
9290
AN XY:
74400
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
425
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at