Variant 1-3682346-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005427.4(TP73):c.-20C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,513,362 control chromosomes in the GnomAD database, including 32,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.19 ( 2804 hom., cov: 34)

Exomes 𝑓: 0.21 ( 29518 hom. )

Consequence

TP73
NM_005427.4 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.956

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 1-3682346-C-T is Benign according to our data. Variant chr1-3682346-C-T is described in ClinVar as [Benign]. Clinvar id is 2585655.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.268 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.-20C>T		5_prime_UTR_variant	2/14	ENST00000378295.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TP73	ENST00000378295.9 linkuse as main transcript	c.-20C>T		5_prime_UTR_variant	2/14	1	NM_005427.4	P1	O15350-1

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28323

AN:

152084

Hom.:

2801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.216

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.196

GnomAD3 exomes

AF:

0.202

AC:

30400

AN:

150652

Hom.:

3210

AF XY:

0.196

AC XY:

15767

AN XY:

80384

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.278

Gnomad ASJ exome

AF:

0.206

Gnomad EAS exome

AF:

0.226

Gnomad SAS exome

AF:

0.133

Gnomad FIN exome

AF:

0.182

Gnomad NFE exome

AF:

0.207

Gnomad OTH exome

AF:

0.206

GnomAD4 exome

AF:

0.205

AC:

279644

AN:

1361158

Hom.:

29518

Cov.:

AF XY:

0.203

AC XY:

136017

AN XY:

669512

show subpopulations

Gnomad4 AFR exome

AF:

0.123

Gnomad4 AMR exome

AF:

0.281

Gnomad4 ASJ exome

AF:

0.201

Gnomad4 EAS exome

AF:

0.239

Gnomad4 SAS exome

AF:

0.137

Gnomad4 FIN exome

AF:

0.179

Gnomad4 NFE exome

AF:

0.211

Gnomad4 OTH exome

AF:

0.205

GnomAD4 genome

AF:

0.186

AC:

28344

AN:

152204

Hom.:

2804

Cov.:

AF XY:

0.188

AC XY:

13961

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.128

Gnomad4 AMR

AF:

0.275

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.217

Gnomad4 SAS

AF:

0.141

Gnomad4 FIN

AF:

0.187

Gnomad4 NFE

AF:

0.203

Gnomad4 OTH

AF:

0.194

Alfa

AF:

0.188

Hom.:

593

Bravo

AF:

0.193

Asia WGS

AF:

0.172

AC:

597

AN:

3478

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

-0.85

CADD

Benign

2.1

DANN

Benign

0.60

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