8-70124696-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The ENST00000452400.7(NCOA2):c.4086C>T(p.Gly1362=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000405 in 1,603,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000043 ( 0 hom. )
Consequence
NCOA2
ENST00000452400.7 synonymous
ENST00000452400.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.534
Genes affected
NCOA2 (HGNC:7669): (nuclear receptor coactivator 2) The protein encoded by this gene functions as a transcriptional coactivator for nuclear hormone receptors, including steroid, thyroid, retinoid, and vitamin D receptors. The encoded protein acts as an intermediary factor for the ligand-dependent activity of these nuclear receptors, which regulate their target genes upon binding of cognate response elements. This gene has been found to be involved in translocations that result in fusions with other genes in various cancers, including the lysine acetyltransferase 6A (KAT6A) gene in acute myeloid leukemia, the ETS variant 6 (ETV6) gene in acute lymphoblastic leukemia, and the hes related family bHLH transcription factor with YRPW motif 1 (HEY1) gene in mesenchymal chondrosarcoma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 8-70124696-G-A is Benign according to our data. Variant chr8-70124696-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 760989.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.534 with no splicing effect.
BS2
High AC in GnomAdExome4 at 63 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NCOA2 | NM_006540.4 | c.4086C>T | p.Gly1362= | synonymous_variant | 20/23 | ENST00000452400.7 | NP_006531.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NCOA2 | ENST00000452400.7 | c.4086C>T | p.Gly1362= | synonymous_variant | 20/23 | 1 | NM_006540.4 | ENSP00000399968 | P1 | |
NCOA2 | ENST00000518363.2 | c.1464C>T | p.Gly488= | synonymous_variant | 8/11 | 2 | ENSP00000429132 | |||
NCOA2 | ENST00000518287.6 | c.*1043C>T | 3_prime_UTR_variant, NMD_transcript_variant | 19/21 | 5 | ENSP00000430148 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152040Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000434 AC: 63AN: 1451048Hom.: 0 Cov.: 30 AF XY: 0.0000402 AC XY: 29AN XY: 721622
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152040Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74276
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 19, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at