22-40251193-A-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4BP6_ModerateBS1BS2

The NM_001162501.2(TNRC6B):c.108A>C(p.Lys36Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000383 in 1,535,714 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

Genomes: 𝑓 0.00021 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00040 ( 0 hom. )

Consequence

TNRC6B
NM_001162501.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.21

Variant links:

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]

TNRC6B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.28448594).

BP6

Variant 22-40251193-A-C is Benign according to our data. Variant chr22-40251193-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 3026122.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00021 (32/152172) while in subpopulation NFE AF= 0.000294 (20/68042). AF 95% confidence interval is 0.000194. There are 0 homozygotes in gnomad4. There are 10 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High AC in GnomAd at 32 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TNRC6B	NM_001162501.2 linkuse as main transcript	c.108A>C	p.Lys36Asn	missense_variant	3/23	ENST00000454349.7
TNRC6B	NM_015088.3 linkuse as main transcript	c.108A>C	p.Lys36Asn	missense_variant	3/21
TNRC6B	NM_001024843.2 linkuse as main transcript	c.216A>C	p.Lys72Asn	missense_variant	6/24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNRC6B	ENST00000454349.7 linkuse as main transcript	c.108A>C	p.Lys36Asn	missense_variant	3/23	2	NM_001162501.2	P3	Q9UPQ9-3
TNRC6B	ENST00000335727.13 linkuse as main transcript	c.108A>C	p.Lys36Asn	missense_variant	3/21	1			Q9UPQ9-1
TNRC6B	ENST00000402203.5 linkuse as main transcript	c.216A>C	p.Lys72Asn	missense_variant	6/24	1		A2	Q9UPQ9-2
TNRC6B	ENST00000301923.13 linkuse as main transcript	c.216A>C	p.Lys72Asn	missense_variant	6/24	5		A2	Q9UPQ9-2

Frequencies

GnomAD3 genomes

AF:

0.000210

AC:

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000265

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000294

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000121

AC:

AN:

148536

Hom.:

AF XY:

0.000101

AC XY:

AN XY:

79084

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000291

Gnomad OTH exome

AF:

0.000240

GnomAD4 exome

AF:

0.000402

AC:

556

AN:

1383542

Hom.:

Cov.:

AF XY:

0.000357

AC XY:

244

AN XY:

682714

show subpopulations

Gnomad4 AFR exome

AF:

0.0000324

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000479

Gnomad4 OTH exome

AF:

0.000734

GnomAD4 genome

AF:

0.000210

AC:

AN:

152172

Hom.:

Cov.:

AF XY:

0.000135

AC XY:

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.000265

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000294

Gnomad4 OTH

AF:

0.000478

Alfa

AF:

0.000358

Hom.:

Bravo

AF:

0.000246

ExAC

AF:

0.0000366

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2023

TNRC6B: BS1 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.84

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.42

Cadd

Uncertain

Dann

Uncertain

1.0

Eigen

Uncertain

0.62

Eigen_PC

Uncertain

0.64

FATHMM_MKL

Uncertain

0.86

LIST_S2

Uncertain

0.95

D;.;D;D

M_CAP

Benign

0.012

MetaRNN

Benign

0.28

T;T;T;T

MetaSVM

Benign

-0.98

MutationTaster

Benign

0.98

D;D;N;N

PrimateAI

Pathogenic

0.86

PROVEAN

Benign

0.050

N;N;N;N

REVEL

Benign

0.11

Sift

Pathogenic

0.0

D;D;D;D

Sift4G

Benign

0.44

T;T;D;D

Polyphen

0.99

D;D;D;D

Vest4

0.52

MutPred

0.30

.;.;Loss of methylation at K36 (P = 7e-04);Loss of methylation at K36 (P = 7e-04);

MVP

0.42

MPC

0.17

ClinPred

0.20

GERP RS

5.7

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.6

Varity_R

0.26

gMVP

0.22

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over