11-64314317-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_004451.5(ESRRA):​c.521G>A​(p.Gly174Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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: 6.9e-7 ( 0 hom. )

Consequence

ESRRA
NM_004451.5 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.670
Variant links:
Genes affected
ESRRA (HGNC:3471): (estrogen related receptor alpha) The protein encoded by this gene is a nuclear receptor that is most closely related to the estrogen receptor. This protein acts as a site-specific transcription factor and interacts with members of the PGC-1 family of transcription cofactors to regulate the expression of most genes involved in cellular energy production as well as in the process of mitochondrial biogenesis. A processed pseudogene of ESRRA is located on chromosome 13q12.1. [provided by RefSeq, Jun 2019]

Genome browser will be placed here

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=0.18986827).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ESRRANM_004451.5 linkuse as main transcriptc.521G>A p.Gly174Asp missense_variant 4/7 ENST00000000442.11 NP_004442.3 P11474-1Q569H8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ESRRAENST00000000442.11 linkuse as main transcriptc.521G>A p.Gly174Asp missense_variant 4/71 NM_004451.5 ENSP00000000442.6 P11474-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.87e-7
AC:
1
AN:
1455176
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
723382
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.01e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

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 submitterclinical testingAmbry GeneticsDec 20, 2023The c.521G>A (p.G174D) alteration is located in exon 4 (coding exon 3) of the ESRRA gene. This alteration results from a G to A substitution at nucleotide position 521, causing the glycine (G) at amino acid position 174 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.28
BayesDel_addAF
Uncertain
0.043
T
BayesDel_noAF
Benign
-0.18
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.066
.;T;.;T
Eigen
Benign
-0.095
Eigen_PC
Benign
-0.0049
FATHMM_MKL
Benign
0.59
D
LIST_S2
Benign
0.55
T;.;T;T
M_CAP
Uncertain
0.16
D
MetaRNN
Benign
0.19
T;T;T;T
MetaSVM
Uncertain
0.25
D
MutationAssessor
Benign
0.97
L;L;.;L
PrimateAI
Uncertain
0.71
T
PROVEAN
Benign
0.23
N;N;N;N
REVEL
Benign
0.24
Sift
Benign
0.44
T;T;T;T
Sift4G
Benign
0.57
T;T;T;T
Polyphen
0.74
P;B;.;B
Vest4
0.24
MutPred
0.27
Loss of catalytic residue at G174 (P = 0.0537);Loss of catalytic residue at G174 (P = 0.0537);.;Loss of catalytic residue at G174 (P = 0.0537);
MVP
0.76
MPC
0.81
ClinPred
0.30
T
GERP RS
4.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.072
gMVP
0.77

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1157602596; hg19: chr11-64081789; COSMIC: COSV50004893; COSMIC: COSV50004893; API