Variant chr22-36476703-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_012473.4(TXN2):c.387+30A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.773 in 1,613,398 control chromosomes in the GnomAD database, including 492,175 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.76 ( 45329 hom., cov: 30)

Exomes 𝑓: 0.77 ( 446846 hom. )

Consequence

TXN2
NM_012473.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.571

Variant links:

Genes affected

TXN2 (HGNC:17772): (thioredoxin 2) This nuclear gene encodes a mitochondrial member of the thioredoxin family, a group of small multifunctional redox-active proteins. The encoded protein may play important roles in the regulation of the mitochondrial membrane potential and in protection against oxidant-induced apoptosis. [provided by RefSeq, Jul 2008]

TXN2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 22-36476703-T-G is Benign according to our data. Variant chr22-36476703-T-G is described in ClinVar as [Benign]. Clinvar id is 1280669.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TXN2	NM_012473.4 linkuse as main transcript	c.387+30A>C		intron_variant		ENST00000216185.7
TXN2	XM_006724226.2 linkuse as main transcript	c.387+30A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TXN2	ENST00000216185.7 linkuse as main transcript	c.387+30A>C		intron_variant		1	NM_012473.4	P1

Frequencies

GnomAD3 genomes

AF:

0.764

AC:

116052

AN:

151890

Hom.:

45302

Cov.:

show subpopulations

Gnomad AFR

AF:

0.769

Gnomad AMI

AF:

0.868

Gnomad AMR

AF:

0.795

Gnomad ASJ

AF:

0.799

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.520

Gnomad FIN

AF:

0.723

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.813

Gnomad OTH

AF:

0.771

GnomAD3 exomes

AF:

0.719

AC:

180359

AN:

250778

Hom.:

67935

AF XY:

0.714

AC XY:

96711

AN XY:

135534

show subpopulations

Gnomad AFR exome

AF:

0.771

Gnomad AMR exome

AF:

0.758

Gnomad ASJ exome

AF:

0.789

Gnomad EAS exome

AF:

0.266

Gnomad SAS exome

AF:

0.548

Gnomad FIN exome

AF:

0.724

Gnomad NFE exome

AF:

0.811

Gnomad OTH exome

AF:

0.754

GnomAD4 exome

AF:

0.774

AC:

1131615

AN:

1461390

Hom.:

446846

Cov.:

AF XY:

0.769

AC XY:

558835

AN XY:

727020

show subpopulations

Gnomad4 AFR exome

AF:

0.770

Gnomad4 AMR exome

AF:

0.764

Gnomad4 ASJ exome

AF:

0.781

Gnomad4 EAS exome

AF:

0.287

Gnomad4 SAS exome

AF:

0.558

Gnomad4 FIN exome

AF:

0.735

Gnomad4 NFE exome

AF:

0.812

Gnomad4 OTH exome

AF:

0.748

GnomAD4 genome

AF:

0.764

AC:

116134

AN:

152008

Hom.:

45329

Cov.:

AF XY:

0.755

AC XY:

56100

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.769

Gnomad4 AMR

AF:

0.795

Gnomad4 ASJ

AF:

0.799

Gnomad4 EAS

AF:

0.259

Gnomad4 SAS

AF:

0.520

Gnomad4 FIN

AF:

0.723

Gnomad4 NFE

AF:

0.813

Gnomad4 OTH

AF:

0.765

Alfa

AF:

0.798

Hom.:

50118

Bravo

AF:

0.771

Asia WGS

AF:

0.421

AC:

1465

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Combined oxidative phosphorylation deficiency 29

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.91

DANN

Benign

0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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