chr22-40261881-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001162501.2(TNRC6B):c.165A>G(p.Pro55=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000695 in 1,439,530 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
Consequence
NM_001162501.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNRC6B | NM_001162501.2 | c.165A>G | p.Pro55= | synonymous_variant | 4/23 | ENST00000454349.7 | |
LOC124905121 | XR_007068107.1 | n.304-1513T>C | intron_variant, non_coding_transcript_variant | ||||
TNRC6B | NM_015088.3 | c.165A>G | p.Pro55= | synonymous_variant | 4/21 | ||
TNRC6B | NM_001024843.2 | c.273A>G | p.Pro91= | synonymous_variant | 7/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6B | ENST00000454349.7 | c.165A>G | p.Pro55= | synonymous_variant | 4/23 | 2 | NM_001162501.2 | P3 | |
TNRC6B | ENST00000335727.13 | c.165A>G | p.Pro55= | synonymous_variant | 4/21 | 1 | |||
TNRC6B | ENST00000402203.5 | c.273A>G | p.Pro91= | synonymous_variant | 7/24 | 1 | A2 | ||
TNRC6B | ENST00000301923.13 | c.273A>G | p.Pro91= | synonymous_variant | 7/24 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.95e-7 AC: 1AN: 1439530Hom.: 0 Cov.: 30 AF XY: 0.00000140 AC XY: 1AN XY: 712520
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
TNRC6B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 26, 2022 | 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.