chr17-1361027-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006761.5(YWHAE):c.578+65C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00718 in 1,485,658 control chromosomes in the GnomAD database, including 635 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.037 ( 352 hom., cov: 31)
Exomes 𝑓: 0.0037 ( 283 hom. )
Consequence
YWHAE
NM_006761.5 intron
NM_006761.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.136
Genes affected
YWHAE (HGNC:12851): (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon) This gene product belongs to the 14-3-3 family of proteins which mediate signal transduction by binding to phosphoserine-containing proteins. This highly conserved protein family is found in both plants and mammals, and this protein is 100% identical to the mouse ortholog. It interacts with CDC25 phosphatases, RAF1 and IRS1 proteins, suggesting its role in diverse biochemical activities related to signal transduction, such as cell division and regulation of insulin sensitivity. It has also been implicated in the pathogenesis of small cell lung cancer. Two transcript variants, one protein-coding and the other non-protein-coding, have been found for this gene. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 17-1361027-G-A is Benign according to our data. Variant chr17-1361027-G-A is described in ClinVar as [Benign]. Clinvar id is 1251628.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YWHAE | NM_006761.5 | c.578+65C>T | intron_variant | ENST00000264335.13 | |||
YWHAE | NR_024058.2 | n.723+65C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YWHAE | ENST00000264335.13 | c.578+65C>T | intron_variant | 1 | NM_006761.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0372 AC: 5662AN: 152036Hom.: 352 Cov.: 31
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GnomAD4 exome AF: 0.00375 AC: 4996AN: 1333504Hom.: 283 AF XY: 0.00329 AC XY: 2199AN XY: 667844
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GnomAD4 genome ? AF: 0.0373 AC: 5671AN: 152154Hom.: 352 Cov.: 31 AF XY: 0.0362 AC XY: 2691AN XY: 74400
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 17, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at