Variant 19-47802333-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001397346.1(TPRX1):c.843A>G(p.Pro281=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,301,956 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00013 ( 0 hom., cov: 28)

Exomes 𝑓: 0.00020 ( 4 hom. )

Failed GnomAD Quality Control

Consequence

TPRX1
NM_001397346.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.82

Variant links:

Genes affected

TPRX1 (HGNC:32174): (tetrapeptide repeat homeobox 1) Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain. This gene is a member of the TPRX homeobox gene family. [provided by RefSeq, Jul 2008]

TPRX1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 19-47802333-T-C is Benign according to our data. Variant chr19-47802333-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2650193.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.82 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TPRX1	NM_001397346.1 linkuse as main transcript	c.843A>G	p.Pro281=	synonymous_variant	3/3	ENST00000698655.1	NP_001384275.1
TPRX1	NM_198479.3 linkuse as main transcript	c.969A>G	p.Pro323=	synonymous_variant	4/4		NP_940881.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TPRX1	ENST00000698655.1 linkuse as main transcript	c.843A>G	p.Pro281=	synonymous_variant	3/3		NM_001397346.1	ENSP00000513863	A2
TPRX1	ENST00000535759.2 linkuse as main transcript	c.969A>G	p.Pro323=	synonymous_variant	4/4	1		ENSP00000438832	A2
TPRX1	ENST00000322175.8 linkuse as main transcript	c.605-110A>G		intron_variant		1		ENSP00000513867	P4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

142438

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000162

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000689

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000207

Gnomad SAS

AF:

0.00155

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000303

Gnomad OTH

AF:

0.000509

GnomAD3 exomes

AF:

0.000507

AC:

AN:

151864

Hom.:

AF XY:

0.000707

AC XY:

AN XY:

80586

show subpopulations

Gnomad AFR exome

AF:

0.000266

Gnomad AMR exome

AF:

0.0000410

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000178

Gnomad SAS exome

AF:

0.00272

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000155

Gnomad OTH exome

AF:

0.000231

GnomAD4 exome

AF:

0.000195

AC:

254

AN:

1301956

Hom.:

Cov.:

AF XY:

0.000271

AC XY:

174

AN XY:

642740

show subpopulations

Gnomad4 AFR exome

AF:

0.000256

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000985

Gnomad4 SAS exome

AF:

0.00271

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000355

Gnomad4 OTH exome

AF:

0.000170

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000126

AC:

AN:

142512

Hom.:

Cov.:

AF XY:

0.0000865

AC XY:

AN XY:

69334

show subpopulations

Gnomad4 AFR

AF:

0.000162

Gnomad4 AMR

AF:

0.0000688

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000207

Gnomad4 SAS

AF:

0.00156

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000303

Gnomad4 OTH

AF:

0.000504

Alfa

AF:

0.000424

Hom.:

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

Oct 01, 2022

TPRX1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.2

DANN

Benign

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over