6-125889595-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_181782.5(NCOA7):c.1541A>G(p.His514Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000137 in 1,461,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
NCOA7
NM_181782.5 missense
NM_181782.5 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 3.79
Genes affected
NCOA7 (HGNC:21081): (nuclear receptor coactivator 7) Enables nuclear receptor binding activity and nuclear receptor coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.07792178).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOA7 | NM_181782.5 | c.1541A>G | p.His514Arg | missense_variant | 9/16 | ENST00000392477.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOA7 | ENST00000392477.7 | c.1541A>G | p.His514Arg | missense_variant | 9/16 | 1 | NM_181782.5 | ||
NCOA7 | ENST00000368357.7 | c.1541A>G | p.His514Arg | missense_variant | 10/17 | 1 | |||
NCOA7 | ENST00000229634.13 | c.1196A>G | p.His399Arg | missense_variant | 8/15 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 249800Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135314
GnomAD3 exomes
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249800
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AN XY:
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GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461602Hom.: 0 Cov.: 34 AF XY: 0.0000248 AC XY: 18AN XY: 727104
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727104
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ExAC
?
AF:
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3
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2022 | The c.1541A>G (p.H514R) alteration is located in exon 11 (coding exon 8) of the NCOA7 gene. This alteration results from a A to G substitution at nucleotide position 1541, causing the histidine (H) at amino acid position 514 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
B;B;.
Vest4
MutPred
Gain of disorder (P = 0.0915);Gain of disorder (P = 0.0915);.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
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Score
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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