Variant rs9662633 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005427.4(TP73):c.1830G>A(p.Ala610=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 1,579,402 control chromosomes in the GnomAD database, including 3,138 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.081 ( 802 hom., cov: 33)

Exomes 𝑓: 0.046 ( 2336 hom. )

Consequence

TP73
NM_005427.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.97

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP7

Synonymous conserved (PhyloP=-3.97 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TP73	NM_005427.4 linkuse as main transcript	c.1830G>A	p.Ala610=	synonymous_variant	14/14	ENST00000378295.9	NP_005418.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TP73	ENST00000378295.9 linkuse as main transcript	c.1830G>A	p.Ala610=	synonymous_variant	14/14	1	NM_005427.4	ENSP00000367545	P1	O15350-1

Frequencies

GnomAD3 genomes

AF:

0.0809

AC:

12311

AN:

152082

Hom.:

796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.0403

Gnomad ASJ

AF:

0.0487

Gnomad EAS

AF:

0.223

Gnomad SAS

AF:

0.0524

Gnomad FIN

AF:

0.0515

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0400

Gnomad OTH

AF:

0.0606

GnomAD3 exomes

AF:

0.0643

AC:

11998

AN:

186522

Hom.:

675

AF XY:

0.0618

AC XY:

6304

AN XY:

102020

show subpopulations

Gnomad AFR exome

AF:

0.167

Gnomad AMR exome

AF:

0.0260

Gnomad ASJ exome

AF:

0.0533

Gnomad EAS exome

AF:

0.232

Gnomad SAS exome

AF:

0.0504

Gnomad FIN exome

AF:

0.0539

Gnomad NFE exome

AF:

0.0427

Gnomad OTH exome

AF:

0.0520

GnomAD4 exome

AF:

0.0458

AC:

65402

AN:

1427202

Hom.:

2336

Cov.:

AF XY:

0.0455

AC XY:

32198

AN XY:

708100

show subpopulations

Gnomad4 AFR exome

AF:

0.164

Gnomad4 AMR exome

AF:

0.0278

Gnomad4 ASJ exome

AF:

0.0511

Gnomad4 EAS exome

AF:

0.162

Gnomad4 SAS exome

AF:

0.0487

Gnomad4 FIN exome

AF:

0.0573

Gnomad4 NFE exome

AF:

0.0372

Gnomad4 OTH exome

AF:

0.0628

GnomAD4 genome

AF:

0.0812

AC:

12353

AN:

152200

Hom.:

802

Cov.:

AF XY:

0.0814

AC XY:

6056

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.0403

Gnomad4 ASJ

AF:

0.0487

Gnomad4 EAS

AF:

0.222

Gnomad4 SAS

AF:

0.0516

Gnomad4 FIN

AF:

0.0515

Gnomad4 NFE

AF:

0.0400

Gnomad4 OTH

AF:

0.0643

Alfa

AF:

0.0447

Hom.:

294

Bravo

AF:

0.0845

Asia WGS

AF:

0.130

AC:

451

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.8

DANN

Benign

0.95

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