chr2-24673385-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_003743.5(NCOA1):c.276C>T(p.Asp92=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000591 in 1,573,364 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000058 ( 1 hom. )
Consequence
NCOA1
NM_003743.5 synonymous
NM_003743.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0330
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 made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.33).
BP6
?
Variant 2-24673385-C-T is Benign according to our data. Variant chr2-24673385-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3041101.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.033 with no splicing effect.
BS2
?
High AC in GnomAd at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOA1 | NM_003743.5 | c.276C>T | p.Asp92= | synonymous_variant | 7/23 | ENST00000348332.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOA1 | ENST00000348332.8 | c.276C>T | p.Asp92= | synonymous_variant | 7/23 | 1 | NM_003743.5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152042Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000135 AC: 30AN: 221808Hom.: 1 AF XY: 0.000174 AC XY: 21AN XY: 120386
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GnomAD4 exome AF: 0.0000584 AC: 83AN: 1421204Hom.: 1 Cov.: 29 AF XY: 0.0000723 AC XY: 51AN XY: 704908
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GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74396
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
NCOA1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 14, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at