chr22-40261883-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001162501.2(TNRC6B):c.167T>C(p.Ile56Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000628 in 1,591,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I56V) has been classified as Likely benign.
Frequency
Consequence
NM_001162501.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNRC6B | NM_001162501.2 | c.167T>C | p.Ile56Thr | missense_variant | 4/23 | ENST00000454349.7 | |
LOC124905121 | XR_007068107.1 | n.304-1515A>G | intron_variant, non_coding_transcript_variant | ||||
TNRC6B | NM_015088.3 | c.167T>C | p.Ile56Thr | missense_variant | 4/21 | ||
TNRC6B | NM_001024843.2 | c.275T>C | p.Ile92Thr | missense_variant | 7/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6B | ENST00000454349.7 | c.167T>C | p.Ile56Thr | missense_variant | 4/23 | 2 | NM_001162501.2 | P3 | |
TNRC6B | ENST00000335727.13 | c.167T>C | p.Ile56Thr | missense_variant | 4/21 | 1 | |||
TNRC6B | ENST00000402203.5 | c.275T>C | p.Ile92Thr | missense_variant | 7/24 | 1 | A2 | ||
TNRC6B | ENST00000301923.13 | c.275T>C | p.Ile92Thr | missense_variant | 7/24 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000556 AC: 8AN: 1439492Hom.: 0 Cov.: 30 AF XY: 0.00000421 AC XY: 3AN XY: 712514
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
TNRC6B-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 17, 2023 | The TNRC6B c.167T>C variant is predicted to result in the amino acid substitution p.Ile56Thr. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at