Variant 3-14064854-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NR_002223.3(TPRXL):n.1133C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000083 in 72,294 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 0.000083 ( 0 hom., cov: 23)

Exomes 𝑓: 0.00016 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TPRXL
NR_002223.3 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -4.86

Variant links:

Genes affected

TPRXL (HGNC:):

TPRXL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 3-14064854-C-T is Benign according to our data. Variant chr3-14064854-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2653576.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TPRXL	NR_002223.3 linkuse as main transcript	n.1133C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
TPRXL	ENST00000326972.12 linkuse as main transcript	n.1039C>T	non_coding_transcript_exon_variant	3/3	2
TPRXL	ENST00000424053.5 linkuse as main transcript	n.1225C>T	non_coding_transcript_exon_variant	3/3	3
TPRXL	ENST00000429201.6 linkuse as main transcript	n.1125C>T	non_coding_transcript_exon_variant	4/4	2

Frequencies

GnomAD3 genomes

AF:

0.0000830

AC:

AN:

72294

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000168

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:

0.0000335

Gnomad OTH

AF:

0.00107

GnomAD3 exomes

AF:

0.000193

AC:

AN:

93336

Hom.:

AF XY:

0.000178

AC XY:

AN XY:

50432

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.000504

Gnomad EAS exome

AF:

0.000853

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000938

Gnomad NFE exome

AF:

0.000133

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000160

AC:

AN:

156510

Hom.:

Cov.:

AF XY:

0.000161

AC XY:

AN XY:

87144

show subpopulations

Gnomad4 AFR exome

AF:

0.000178

Gnomad4 AMR exome

AF:

0.000155

Gnomad4 ASJ exome

AF:

0.000211

Gnomad4 EAS exome

AF:

0.000581

Gnomad4 SAS exome

AF:

0.0000676

Gnomad4 FIN exome

AF:

0.000805

Gnomad4 NFE exome

AF:

0.0000986

Gnomad4 OTH exome

AF:

0.000263

GnomAD4 genome

AF:

0.0000830

AC:

AN:

72294

Hom.:

Cov.:

AF XY:

0.0000856

AC XY:

AN XY:

35048

show subpopulations

Gnomad4 AFR

AF:

0.000168

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:

0.0000335

Gnomad4 OTH

AF:

0.00107

Alfa

AF:

0.0522

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

TPRXL: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

3.5

DANN

Benign

0.41

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