chr3-32818317-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001039111.3(TRIM71):c.237C>T(p.Gly79=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000447 in 1,436,742 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00022 ( 1 hom. )
Consequence
TRIM71
NM_001039111.3 synonymous
NM_001039111.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.82
Genes affected
TRIM71 (HGNC:32669): (tripartite motif containing 71) The protein encoded by this gene is an E3 ubiquitin-protein ligase that binds with miRNAs and maintains the growth and upkeep of embryonic stem cells. This gene also is involved in the G1-S phase transition of the cell cycle. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
Variant 3-32818317-C-T is Benign according to our data. Variant chr3-32818317-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 712982.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.82 with no splicing effect.
BS2
High AC in GnomAd4 at 355 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM71 | NM_001039111.3 | c.237C>T | p.Gly79= | synonymous_variant | 1/4 | ENST00000383763.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM71 | ENST00000383763.6 | c.237C>T | p.Gly79= | synonymous_variant | 1/4 | 1 | NM_001039111.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00236 AC: 356AN: 150550Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000219 AC: 14AN: 64014Hom.: 0 AF XY: 0.000212 AC XY: 8AN XY: 37758
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GnomAD4 exome AF: 0.000223 AC: 287AN: 1286084Hom.: 1 Cov.: 31 AF XY: 0.000229 AC XY: 145AN XY: 634360
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GnomAD4 genome AF: 0.00236 AC: 355AN: 150658Hom.: 1 Cov.: 33 AF XY: 0.00223 AC XY: 164AN XY: 73568
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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 16, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at