3-32818179-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001039111.3(TRIM71):c.99G>C(p.Ser33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000269 in 1,599,398 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 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000028 ( 0 hom. )
Consequence
TRIM71
NM_001039111.3 synonymous
NM_001039111.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.912
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=-0.61).
BP6
?
Variant 3-32818179-G-C is Benign according to our data. Variant chr3-32818179-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3037046.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.912 with no splicing effect.
BS2
?
High AC in GnomAdExome at 38 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM71 | NM_001039111.3 | c.99G>C | p.Ser33= | synonymous_variant | 1/4 | ENST00000383763.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM71 | ENST00000383763.6 | c.99G>C | p.Ser33= | synonymous_variant | 1/4 | 1 | NM_001039111.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151976Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000166 AC: 38AN: 229084Hom.: 0 AF XY: 0.000142 AC XY: 18AN XY: 126476
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GnomAD4 exome AF: 0.0000283 AC: 41AN: 1447422Hom.: 0 Cov.: 31 AF XY: 0.0000250 AC XY: 18AN XY: 720142
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151976Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74218
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TRIM71-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 24, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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