rs116803435
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001379180.1(ESRRB):c.1120+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000231 in 1,566,922 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 0.0012 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00013 ( 1 hom. )
Consequence
ESRRB
NM_001379180.1 intron
NM_001379180.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.54
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 14-76491727-C-T is Benign according to our data. Variant chr14-76491727-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 227362.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00116 (176/152328) while in subpopulation AFR AF= 0.00406 (169/41578). AF 95% confidence interval is 0.00356. There are 0 homozygotes in gnomad4. There are 83 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ESRRB | NM_001379180.1 | c.1120+11C>T | intron_variant | ENST00000644823.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ESRRB | ENST00000644823.1 | c.1120+11C>T | intron_variant | NM_001379180.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00116 AC: 176AN: 152210Hom.: 0 Cov.: 34
GnomAD3 genomes
?
AF:
AC:
176
AN:
152210
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000354 AC: 62AN: 175266Hom.: 0 AF XY: 0.000258 AC XY: 24AN XY: 93120
GnomAD3 exomes
AF:
AC:
62
AN:
175266
Hom.:
AF XY:
AC XY:
24
AN XY:
93120
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000131 AC: 186AN: 1414594Hom.: 1 Cov.: 35 AF XY: 0.000113 AC XY: 79AN XY: 698828
GnomAD4 exome
AF:
AC:
186
AN:
1414594
Hom.:
Cov.:
35
AF XY:
AC XY:
79
AN XY:
698828
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00116 AC: 176AN: 152328Hom.: 0 Cov.: 34 AF XY: 0.00111 AC XY: 83AN XY: 74488
GnomAD4 genome
?
AF:
AC:
176
AN:
152328
Hom.:
Cov.:
34
AF XY:
AC XY:
83
AN XY:
74488
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | 1057+11C>T in Intron 08 of ESRRB: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus seq uence and has been identified in 0.3% (10/3704) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.was hington.edu/EVS; dbSNP rs116803435). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at