rs201417586
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001379180.1(ESRRB):c.876C>T(p.Asp292=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000256 in 1,608,198 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00023 ( 1 hom., cov: 34)
Exomes 𝑓: 0.00026 ( 3 hom. )
Consequence
ESRRB
NM_001379180.1 synonymous
NM_001379180.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.60
Genes affected
ESRRB (HGNC:3473): (estrogen related receptor beta) This gene encodes a protein with similarity to the estrogen receptor. Its function is unknown; however, a similar protein in mouse plays an essential role in placental development. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
Variant 14-76491472-C-T is Benign according to our data. Variant chr14-76491472-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 226637.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=2.6 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ESRRB | NM_001379180.1 | c.876C>T | p.Asp292= | synonymous_variant | 6/7 | ENST00000644823.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ESRRB | ENST00000644823.1 | c.876C>T | p.Asp292= | synonymous_variant | 6/7 | NM_001379180.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152262Hom.: 1 Cov.: 34
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GnomAD3 exomes AF: 0.000422 AC: 101AN: 239198Hom.: 3 AF XY: 0.000634 AC XY: 82AN XY: 129400
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GnomAD4 exome AF: 0.000258 AC: 376AN: 1455818Hom.: 3 Cov.: 41 AF XY: 0.000344 AC XY: 249AN XY: 723700
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GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152380Hom.: 1 Cov.: 34 AF XY: 0.000268 AC XY: 20AN XY: 74514
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 27, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 15, 2023 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 31, 2016 | p.Asp271Asp in exon 8 of ESRRB: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, it is not located w ithin the splice consensus sequence, and it has been identified in 0.3% (37/1256 8) of South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http:// exac.broadinstitute.org; dbSNP rs201417586). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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