rs4986938
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001437.3(ESR2):c.*39G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,594,296 control chromosomes in the GnomAD database, including 102,226 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.32 ( 8374 hom., cov: 31)
Exomes 𝑓: 0.35 ( 93852 hom. )
Consequence
ESR2
NM_001437.3 3_prime_UTR
NM_001437.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.222
Genes affected
ESR2 (HGNC:3468): (estrogen receptor 2) This gene encodes a member of the family of estrogen receptors and superfamily of nuclear receptor transcription factors. The gene product contains an N-terminal DNA binding domain and C-terminal ligand binding domain and is localized to the nucleus, cytoplasm, and mitochondria. Upon binding to 17beta-estradiol or related ligands, the encoded protein forms homo- or hetero-dimers that interact with specific DNA sequences to activate transcription. Some isoforms dominantly inhibit the activity of other estrogen receptor family members. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been fully characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 14-64233098-C-T is Benign according to our data. Variant chr14-64233098-C-T is described in ClinVar as [Benign]. Clinvar id is 1266011.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ESR2 | NM_001437.3 | c.*39G>A | 3_prime_UTR_variant | 9/9 | ENST00000341099.6 | NP_001428.1 | ||
LOC124903328 | XR_007064205.1 | n.90-1764C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ESR2 | ENST00000341099.6 | c.*39G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_001437.3 | ENSP00000343925 | P1 |
Frequencies
GnomAD3 genomes AF: 0.323 AC: 49115AN: 151878Hom.: 8380 Cov.: 31
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GnomAD3 exomes AF: 0.310 AC: 75935AN: 244898Hom.: 13063 AF XY: 0.318 AC XY: 41985AN XY: 132172
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GnomAD4 exome AF: 0.355 AC: 511822AN: 1442300Hom.: 93852 Cov.: 34 AF XY: 0.354 AC XY: 252570AN XY: 714176
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GnomAD4 genome AF: 0.323 AC: 49123AN: 151996Hom.: 8374 Cov.: 31 AF XY: 0.320 AC XY: 23803AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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