chr17-1361892-T-TA
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_006761.5(YWHAE):c.371+9_371+10insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000305 in 1,574,148 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000030 ( 0 hom. )
Consequence
YWHAE
NM_006761.5 intron
NM_006761.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0900
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 Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 17-1361892-T-TA is Benign according to our data. Variant chr17-1361892-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 1586680.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YWHAE | NM_006761.5 | c.371+9_371+10insT | intron_variant | ENST00000264335.13 | |||
YWHAE | NR_024058.2 | n.516+9_516+10insT | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YWHAE | ENST00000264335.13 | c.371+9_371+10insT | intron_variant | 1 | NM_006761.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152132Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000265 AC: 6AN: 226056Hom.: 0 AF XY: 0.0000406 AC XY: 5AN XY: 123224
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GnomAD4 exome AF: 0.0000302 AC: 43AN: 1422016Hom.: 0 Cov.: 27 AF XY: 0.0000353 AC XY: 25AN XY: 708340
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GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152132Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74334
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2021 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at