chr22-40262052-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001162501.2(TNRC6B):c.336A>G(p.Pro112=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000252 in 1,595,106 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00022 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00026 ( 2 hom. )
Consequence
TNRC6B
NM_001162501.2 synonymous
NM_001162501.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0640
Genes affected
TNRC6B (HGNC:29190): (trinucleotide repeat containing adaptor 6B) Enables RNA binding activity. Involved in regulation of gene expression. Predicted to be located in cytosol. Predicted to be active in P-body and nucleoplasm. Implicated in subserous uterine fibroid and uterine fibroid. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 22-40262052-A-G is Benign according to our data. Variant chr22-40262052-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2653168.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.064 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000217 (33/152204) while in subpopulation SAS AF= 0.000829 (4/4826). AF 95% confidence interval is 0.000283. There are 0 homozygotes in gnomad4. There are 14 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 33 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNRC6B | NM_001162501.2 | c.336A>G | p.Pro112= | synonymous_variant | 4/23 | ENST00000454349.7 | |
LOC124905121 | XR_007068107.1 | n.304-1684T>C | intron_variant, non_coding_transcript_variant | ||||
TNRC6B | NM_015088.3 | c.336A>G | p.Pro112= | synonymous_variant | 4/21 | ||
TNRC6B | NM_001024843.2 | c.444A>G | p.Pro148= | synonymous_variant | 7/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6B | ENST00000454349.7 | c.336A>G | p.Pro112= | synonymous_variant | 4/23 | 2 | NM_001162501.2 | P3 | |
TNRC6B | ENST00000335727.13 | c.336A>G | p.Pro112= | synonymous_variant | 4/21 | 1 | |||
TNRC6B | ENST00000402203.5 | c.444A>G | p.Pro148= | synonymous_variant | 7/24 | 1 | A2 | ||
TNRC6B | ENST00000301923.13 | c.444A>G | p.Pro148= | synonymous_variant | 7/24 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152086Hom.: 0 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
33
AN:
152086
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000387 AC: 87AN: 224724Hom.: 0 AF XY: 0.000468 AC XY: 57AN XY: 121850
GnomAD3 exomes
AF:
AC:
87
AN:
224724
Hom.:
AF XY:
AC XY:
57
AN XY:
121850
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000256 AC: 369AN: 1442902Hom.: 2 Cov.: 30 AF XY: 0.000274 AC XY: 196AN XY: 715960
GnomAD4 exome
AF:
AC:
369
AN:
1442902
Hom.:
Cov.:
30
AF XY:
AC XY:
196
AN XY:
715960
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000217 AC: 33AN: 152204Hom.: 0 Cov.: 31 AF XY: 0.000188 AC XY: 14AN XY: 74418
GnomAD4 genome
?
AF:
AC:
33
AN:
152204
Hom.:
Cov.:
31
AF XY:
AC XY:
14
AN XY:
74418
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
TNRC6B-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 01, 2019 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | TNRC6B: BP4, BP7 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at