Variant chr1-3722110-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_005427.4(TP73):c.519C>T(p.Thr173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 1,612,596 control chromosomes in the GnomAD database, including 602,217 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.83 ( 52538 hom., cov: 34)

Exomes 𝑓: 0.86 ( 549679 hom. )

Consequence

TP73
NM_005427.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.149

Variant links:

Genes affected

TP73 (HGNC:12003): (tumor protein p73) This gene encodes a member of the p53 family of transcription factors involved in cellular responses to stress and development. It maps to a region on chromosome 1p36 that is frequently deleted in neuroblastoma and other tumors, and thought to contain multiple tumor suppressor genes. The demonstration that this gene is monoallelically expressed (likely from the maternal allele), supports the notion that it is a candidate gene for neuroblastoma. Many transcript variants resulting from alternative splicing and/or use of alternate promoters have been found for this gene, but the biological validity and the full-length nature of some variants have not been determined. [provided by RefSeq, Feb 2011]

TP73 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 1-3722110-C-T is Benign according to our data. Variant chr1-3722110-C-T is described in ClinVar as [Benign]. Clinvar id is 2585656.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.149 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TP73	NM_005427.4 linkuse as main transcript	c.519C>T	p.Thr173=	synonymous_variant	5/14	ENST00000378295.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TP73	ENST00000378295.9 linkuse as main transcript	c.519C>T	p.Thr173=	synonymous_variant	5/14	1	NM_005427.4	P1	O15350-1

Frequencies

GnomAD3 genomes

AF:

0.826

AC:

125563

AN:

152090

Hom.:

52513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.771

Gnomad AMI

AF:

0.975

Gnomad AMR

AF:

0.726

Gnomad ASJ

AF:

0.938

Gnomad EAS

AF:

0.523

Gnomad SAS

AF:

0.743

Gnomad FIN

AF:

0.859

Gnomad MID

AF:

0.949

Gnomad NFE

AF:

0.896

Gnomad OTH

AF:

0.850

GnomAD3 exomes

AF:

0.804

AC:

200645

AN:

249628

Hom.:

82730

AF XY:

0.813

AC XY:

110104

AN XY:

135502

show subpopulations

Gnomad AFR exome

AF:

0.769

Gnomad AMR exome

AF:

0.629

Gnomad ASJ exome

AF:

0.929

Gnomad EAS exome

AF:

0.514

Gnomad SAS exome

AF:

0.761

Gnomad FIN exome

AF:

0.858

Gnomad NFE exome

AF:

0.897

Gnomad OTH exome

AF:

0.852

GnomAD4 exome

AF:

0.863

AC:

1260594

AN:

1460388

Hom.:

549679

Cov.:

AF XY:

0.862

AC XY:

625980

AN XY:

726476

show subpopulations

Gnomad4 AFR exome

AF:

0.764

Gnomad4 AMR exome

AF:

0.641

Gnomad4 ASJ exome

AF:

0.928

Gnomad4 EAS exome

AF:

0.509

Gnomad4 SAS exome

AF:

0.760

Gnomad4 FIN exome

AF:

0.853

Gnomad4 NFE exome

AF:

0.895

Gnomad4 OTH exome

AF:

0.856

GnomAD4 genome

AF:

0.825

AC:

125638

AN:

152208

Hom.:

52538

Cov.:

AF XY:

0.819

AC XY:

60961

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.771

Gnomad4 AMR

AF:

0.726

Gnomad4 ASJ

AF:

0.938

Gnomad4 EAS

AF:

0.522

Gnomad4 SAS

AF:

0.745

Gnomad4 FIN

AF:

0.859

Gnomad4 NFE

AF:

0.896

Gnomad4 OTH

AF:

0.848

Alfa

AF:

0.866

Hom.:

39086

Bravo

AF:

0.812

Asia WGS

AF:

0.632

AC:

2197

AN:

3478

EpiCase

AF:

0.903

EpiControl

AF:

0.907

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Ciliary dyskinesia, primary, 47, and lissencephaly

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

2.1

DANN

Benign

0.94

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