rs1256049
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001437.3(ESR2):c.984G>A(p.Val328=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0661 in 152108 control chromosomes in the gnomAD Genomes database, including 674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (β β ).
Frequency
Genomes: π 0.066 ( 674 hom., cov: 31)
Exomes π: 0.067 ( 1557 hom. )
Consequence
ESR2
NM_001437.3 synonymous
NM_001437.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0340
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant 14-64257333-C-T is Benign according to our data. Variant chr14-64257333-C-T is described in ClinVar as [Benign]. Clinvar id is 1228925. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.034 with no splicing effect.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ESR2 | NM_001437.3 | c.984G>A | p.Val328= | synonymous_variant | 6/9 | ENST00000341099.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ESR2 | ENST00000341099.6 | c.984G>A | p.Val328= | synonymous_variant | 6/9 | 1 | NM_001437.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0661 AC: 10050AN: 152108Hom.: 674 Cov.: 31
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GnomAD3 exomes AF: 0.0667 AC: 16779AN: 251436Hom.: 1557 AF XY: 0.0624 AC XY: 8474AN XY: 135902
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GnomAD4 exome AF: 0.0445 AC: 64963AN: 1461140Hom.: 3351 AF XY: 0.0438 AC XY: 31842AN XY: 726868
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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 | clinical testing | Invitae | Oct 27, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | This variant is associated with the following publications: (PMID: 11231990) - |
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