chr16-24777228-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_014494.4(TNRC6A):c.459G>A(p.Gln153=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 1,614,178 control chromosomes in the GnomAD database, including 140 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 18 hom., cov: 32)
Exomes 𝑓: 0.012 ( 122 hom. )
Consequence
TNRC6A
NM_014494.4 synonymous
NM_014494.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.45
Genes affected
TNRC6A (HGNC:11969): (trinucleotide repeat containing adaptor 6A) This gene encodes a member of the trinucleotide repeat containing 6 protein family. The protein functions in post-transcriptional gene silencing through the RNA interference (RNAi) and microRNA pathways. The protein associates with messenger RNAs and Argonaute proteins in cytoplasmic bodies known as GW-bodies or P-bodies. Inhibiting expression of this gene delocalizes other GW-body proteins and impairs RNAi and microRNA-induced gene silencing. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 16-24777228-G-A is Benign according to our data. Variant chr16-24777228-G-A is described in ClinVar as [Benign]. Clinvar id is 781725.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.45 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0108 (1646/152288) while in subpopulation AMR AF= 0.0197 (301/15300). AF 95% confidence interval is 0.0178. There are 18 homozygotes in gnomad4. There are 796 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1646 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNRC6A | NM_014494.4 | c.459G>A | p.Gln153= | synonymous_variant | 5/25 | ENST00000395799.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6A | ENST00000395799.8 | c.459G>A | p.Gln153= | synonymous_variant | 5/25 | 5 | NM_014494.4 | A2 | |
TNRC6A | ENST00000315183.11 | c.459G>A | p.Gln153= | synonymous_variant | 5/24 | 5 | P4 | ||
TNRC6A | ENST00000491718.5 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0108 AC: 1646AN: 152170Hom.: 18 Cov.: 32
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GnomAD3 exomes AF: 0.00883 AC: 2207AN: 249986Hom.: 17 AF XY: 0.00872 AC XY: 1183AN XY: 135602
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GnomAD4 exome AF: 0.0116 AC: 16901AN: 1461890Hom.: 122 Cov.: 35 AF XY: 0.0114 AC XY: 8259AN XY: 727246
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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