chr2-24755628-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003743.5(NCOA1):c.3882-2345G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0744 in 152,252 control chromosomes in the GnomAD database, including 516 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 0.074 ( 516 hom., cov: 32)
Consequence
NCOA1
NM_003743.5 intron
NM_003743.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.703
Publications
4 publications found
Genes affected
NCOA1 (HGNC:7668): (nuclear receptor coactivator 1) The protein encoded by this gene acts as a transcriptional coactivator for steroid and nuclear hormone receptors. It is a member of the p160/steroid receptor coactivator (SRC) family and like other family members has histone acetyltransferase activity and contains a nuclear localization signal, as well as bHLH and PAS domains. The product of this gene binds nuclear receptors directly and stimulates the transcriptional activities in a hormone-dependent fashion. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -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 = 0.116 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NCOA1 | NM_003743.5 | c.3882-2345G>A | intron_variant | Intron 20 of 22 | ENST00000348332.8 | NP_003734.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0744 AC: 11318AN: 152136Hom.: 517 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
11318
AN:
152136
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0744 AC: 11332AN: 152252Hom.: 516 Cov.: 32 AF XY: 0.0765 AC XY: 5698AN XY: 74442 show subpopulations
GnomAD4 genome
AF:
AC:
11332
AN:
152252
Hom.:
Cov.:
32
AF XY:
AC XY:
5698
AN XY:
74442
show subpopulations
African (AFR)
AF:
AC:
4946
AN:
41522
American (AMR)
AF:
AC:
1114
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
111
AN:
3472
East Asian (EAS)
AF:
AC:
548
AN:
5182
South Asian (SAS)
AF:
AC:
444
AN:
4818
European-Finnish (FIN)
AF:
AC:
664
AN:
10610
Middle Eastern (MID)
AF:
AC:
14
AN:
294
European-Non Finnish (NFE)
AF:
AC:
3226
AN:
68030
Other (OTH)
AF:
AC:
146
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
522
1045
1567
2090
2612
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
134
268
402
536
670
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
378
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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