chr17-40331290-C-T
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_000964.4(RARA):c.72C>T(p.Tyr24=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,614,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00073 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00014 ( 0 hom. )
Consequence
RARA
NM_000964.4 synonymous
NM_000964.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.638
Genes affected
RARA (HGNC:9864): (retinoic acid receptor alpha) This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 17-40331290-C-T is Benign according to our data. Variant chr17-40331290-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 715637.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.638 with no splicing effect.
BS2
High AC in GnomAd4 at 111 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RARA | NM_000964.4 | c.72C>T | p.Tyr24= | synonymous_variant | 2/9 | ENST00000254066.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RARA | ENST00000254066.10 | c.72C>T | p.Tyr24= | synonymous_variant | 2/9 | 1 | NM_000964.4 | P4 | |
RARA | ENST00000425707.7 | c.72C>T | p.Tyr24= | synonymous_variant | 2/7 | 1 | |||
RARA | ENST00000394089.6 | c.72C>T | p.Tyr24= | synonymous_variant | 2/9 | 2 | P4 | ||
RARA | ENST00000577646.5 | c.72C>T | p.Tyr24= | synonymous_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000703 AC: 107AN: 152214Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000211 AC: 53AN: 250996Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135714
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GnomAD4 exome AF: 0.000143 AC: 209AN: 1461766Hom.: 0 Cov.: 31 AF XY: 0.000154 AC XY: 112AN XY: 727188
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GnomAD4 genome AF: 0.000729 AC: 111AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.000671 AC XY: 50AN XY: 74486
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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 | Mar 29, 2018 | - - |
Computational scores
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Benign
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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