rs2038276
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_ModerateBP6_ModerateBP7BS1
The NM_004239.4(TRIP11):c.5169G>A(p.Leu1723=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000669 in 1,613,348 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 Benign (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000069 ( 0 hom. )
Consequence
TRIP11
NM_004239.4 synonymous
NM_004239.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.104
Genes affected
TRIP11 (HGNC:12305): (thyroid hormone receptor interactor 11) This gene was identified based on the interaction of its protein product with thyroid hormone receptor beta. This protein is associated with the Golgi apparatus. The N-terminal region of the protein binds Golgi membranes and the C-terminal region binds the minus ends of microtubules; thus, the protein is thought to play a role in assembly and maintenance of the Golgi ribbon structure around the centrosome. Mutations in this gene cause achondrogenesis type IA.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant 14-91988375-C-T is Benign according to our data. Variant chr14-91988375-C-T is described in ClinVar as [Benign]. Clinvar id is 528893.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.104 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0000691 (101/1461168) while in subpopulation AMR AF= 0.00226 (101/44704). AF 95% confidence interval is 0.0019. There are 0 homozygotes in gnomad4_exome. There are 45 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIP11 | NM_004239.4 | c.5169G>A | p.Leu1723= | synonymous_variant | 16/21 | ENST00000267622.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIP11 | ENST00000267622.8 | c.5169G>A | p.Leu1723= | synonymous_variant | 16/21 | 1 | NM_004239.4 | P1 | |
TRIP11 | ENST00000554357.5 | c.4317G>A | p.Leu1439= | synonymous_variant | 10/15 | 1 | |||
TRIP11 | ENST00000557017.1 | c.417G>A | p.Leu139= | synonymous_variant, NMD_transcript_variant | 4/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152062Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000372 AC: 93AN: 250204Hom.: 0 AF XY: 0.000303 AC XY: 41AN XY: 135278
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GnomAD4 exome AF: 0.0000691 AC: 101AN: 1461168Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 726898
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GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152180Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74392
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Achondrogenesis, type IA Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at