Variant rs3190321 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015914.7(TXNDC11):c.2266G>C(p.Val756Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 1,612,060 control chromosomes in the GnomAD database, including 233,485 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.51 ( 19976 hom., cov: 31)

Exomes 𝑓: 0.54 ( 213509 hom. )

Consequence

TXNDC11
NM_015914.7 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.50

Variant links:

Genes affected

TXNDC11 (HGNC:28030): (thioredoxin domain containing 11) Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TXNDC11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.9213159E-5).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TXNDC11	NM_015914.7 linkuse as main transcript	c.2266G>C	p.Val756Leu	missense_variant	12/12	ENST00000283033.10	NP_056998.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TXNDC11	ENST00000283033.10 linkuse as main transcript	c.2266G>C	p.Val756Leu	missense_variant	12/12	2	NM_015914.7	ENSP00000283033	P2	Q6PKC3-2
TXNDC11	ENST00000356957.7 linkuse as main transcript	c.2347G>C	p.Val783Leu	missense_variant	13/13	1		ENSP00000349439	A2	Q6PKC3-1
TXNDC11	ENST00000570917.5 linkuse as main transcript	n.476G>C		non_coding_transcript_exon_variant	5/5	5

Frequencies

GnomAD3 genomes

AF:

0.506

AC:

76850

AN:

151738

Hom.:

19957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.448

Gnomad AMI

AF:

0.654

Gnomad AMR

AF:

0.398

Gnomad ASJ

AF:

0.684

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.505

Gnomad FIN

AF:

0.538

Gnomad MID

AF:

0.618

Gnomad NFE

AF:

0.556

Gnomad OTH

AF:

0.516

GnomAD3 exomes

AF:

0.500

AC:

125615

AN:

250996

Hom.:

32904

AF XY:

0.510

AC XY:

69220

AN XY:

135730

show subpopulations

Gnomad AFR exome

AF:

0.443

Gnomad AMR exome

AF:

0.299

Gnomad ASJ exome

AF:

0.697

Gnomad EAS exome

AF:

0.420

Gnomad SAS exome

AF:

0.500

Gnomad FIN exome

AF:

0.534

Gnomad NFE exome

AF:

0.558

Gnomad OTH exome

AF:

0.523

GnomAD4 exome

AF:

0.537

AC:

784283

AN:

1460204

Hom.:

213509

Cov.:

AF XY:

0.537

AC XY:

390218

AN XY:

726236

show subpopulations

Gnomad4 AFR exome

AF:

0.443

Gnomad4 AMR exome

AF:

0.312

Gnomad4 ASJ exome

AF:

0.698

Gnomad4 EAS exome

AF:

0.462

Gnomad4 SAS exome

AF:

0.504

Gnomad4 FIN exome

AF:

0.529

Gnomad4 NFE exome

AF:

0.551

Gnomad4 OTH exome

AF:

0.531

GnomAD4 genome

AF:

0.506

AC:

76899

AN:

151856

Hom.:

19976

Cov.:

AF XY:

0.504

AC XY:

37443

AN XY:

74220

show subpopulations

Gnomad4 AFR

AF:

0.448

Gnomad4 AMR

AF:

0.397

Gnomad4 ASJ

AF:

0.684

Gnomad4 EAS

AF:

0.423

Gnomad4 SAS

AF:

0.505

Gnomad4 FIN

AF:

0.538

Gnomad4 NFE

AF:

0.556

Gnomad4 OTH

AF:

0.520

Alfa

AF:

0.562

Hom.:

7896

Bravo

AF:

0.490

TwinsUK

AF:

0.544

AC:

2017

ALSPAC

AF:

0.559

AC:

2153

ESP6500AA

AF:

0.436

AC:

1914

ESP6500EA

AF:

0.542

AC:

4661

ExAC

AF:

0.507

AC:

61502

Asia WGS

AF:

0.478

AC:

1662

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.061

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.65

DEOGEN2

Benign

0.015

.;T

Eigen

Benign

-0.91

Eigen_PC

Benign

-0.64

FATHMM_MKL

Benign

0.30

LIST_S2

Benign

0.051

T;T

MetaRNN

Benign

0.000029

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

-1.6

.;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.31

PROVEAN

Benign

1.1

N;N

REVEL

Benign

0.035

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.042

MPC

0.059

ClinPred

0.0016

GERP RS

3.6

Varity_R

0.042

gMVP

0.46

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over