16-24789652-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014494.4(TNRC6A):c.1010G>A(p.Ser337Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,461,844 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 Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
TNRC6A
NM_014494.4 missense
NM_014494.4 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 9.15
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.07919419).
BS2
?
High AC in GnomAdExome at 18 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNRC6A | NM_014494.4 | c.1010G>A | p.Ser337Asn | missense_variant | 6/25 | ENST00000395799.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6A | ENST00000395799.8 | c.1010G>A | p.Ser337Asn | missense_variant | 6/25 | 5 | NM_014494.4 | A2 | |
TNRC6A | ENST00000491718.5 | c.*535G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/22 | 1 | ||||
TNRC6A | ENST00000315183.11 | c.1010G>A | p.Ser337Asn | missense_variant | 6/24 | 5 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251176Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135774
GnomAD3 exomes
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GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461844Hom.: 0 Cov.: 30 AF XY: 0.00000825 AC XY: 6AN XY: 727224
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
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ExAC
?
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AC:
8
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2023 | The c.1010G>A (p.S337N) alteration is located in exon 6 (coding exon 6) of the TNRC6A gene. This alteration results from a G to A substitution at nucleotide position 1010, causing the serine (S) at amino acid position 337 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;P
Vest4
MutPred
Loss of phosphorylation at S337 (P = 0.0589);Loss of phosphorylation at S337 (P = 0.0589);
MVP
MPC
0.38
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at