rs146351534
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001379180.1(ESRRB):c.1300G>A(p.Val434Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0128 in 1,613,450 control chromosomes in the GnomAD database, including 201 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001379180.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ESRRB | NM_001379180.1 | c.1300G>A | p.Val434Ile | missense_variant | 7/7 | ENST00000644823.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ESRRB | ENST00000644823.1 | c.1300G>A | p.Val434Ile | missense_variant | 7/7 | NM_001379180.1 | P1 | ||
ENST00000554926.1 | n.415-2813C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0108 AC: 1637AN: 152226Hom.: 14 Cov.: 32
GnomAD3 exomes AF: 0.0115 AC: 2872AN: 249282Hom.: 43 AF XY: 0.0116 AC XY: 1569AN XY: 135276
GnomAD4 exome AF: 0.0130 AC: 19017AN: 1461106Hom.: 187 Cov.: 35 AF XY: 0.0128 AC XY: 9328AN XY: 726866
GnomAD4 genome ? AF: 0.0107 AC: 1637AN: 152344Hom.: 14 Cov.: 32 AF XY: 0.0108 AC XY: 803AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | ESRRB: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 26, 2019 | This variant is associated with the following publications: (PMID: 22951369, 29636544) - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 23, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | Val413Ile in Exon 09 of ESRRB: This variant is not expected to have clinical sig nificance because it has been identified in 1.3% (91/7020) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs146351534). - |
Autosomal recessive nonsyndromic hearing loss 35 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at