rs372821099

Variant names:

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2

The ENST00000455263.6(TP53):c.1038G>A(p.Ser346Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000919 in 1,175,560 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 Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.000059 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000097 ( 0 hom. )

Consequence

TP53
ENST00000455263.6 synonymous

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:3

Conservation

PhyloP100: -1.28

Publications

5 publications found

Variant links:

Genes affected

TP53 (HGNC:11998): (tumor protein p53) This gene encodes a tumor suppressor protein containing transcriptional activation, DNA binding, and oligomerization domains. The encoded protein responds to diverse cellular stresses to regulate expression of target genes, thereby inducing cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism. Mutations in this gene are associated with a variety of human cancers, including hereditary cancers such as Li-Fraumeni syndrome. Alternative splicing of this gene and the use of alternate promoters result in multiple transcript variants and isoforms. Additional isoforms have also been shown to result from the use of alternate translation initiation codons from identical transcript variants (PMIDs: 12032546, 20937277). [provided by RefSeq, Dec 2016]

TP53 Gene-Disease associations (from GenCC):

breast cancer
Inheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics
Li-Fraumeni syndrome
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Orphanet
Li-Fraumeni syndrome 1
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp
adrenocortical carcinoma, hereditary
Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics
sarcoma
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
bone marrow failure syndrome 5
Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
colorectal cancer
Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
choroid plexus carcinoma
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TP53 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 17-7673222-C-T is Benign according to our data. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651. Variant chr17-7673222-C-T is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 492651.

BP7

Synonymous conserved (PhyloP=-1.28 with no splicing effect.

BS1

Variant frequency is greater than expected in population sas. GnomAdExome4 allele frequency = 0.0000967 (99/1024290) while in subpopulation SAS AF = 0.000473 (34/71838). AF 95% confidence interval is 0.000348. There are 0 homozygotes in GnomAdExome4. There are 60 alleles in the male GnomAdExome4 subpopulation. Median coverage is 13. This position passed quality control check.

BS2

High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TP53	NM_000546.6 link	c.993+313G>A		intron_variant	Intron 9 of 10	ENST00000269305.9	NP_000537.3	P04637-1K7PPA8Q53GA5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TP53	ENST00000269305.9 link	c.993+313G>A		intron_variant	Intron 9 of 10	1	NM_000546.6	ENSP00000269305.4		P04637-1

Frequencies

GnomAD3 genomes

AF:

0.0000595

AC:

AN:

151174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000486

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.000624

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000442

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000112

AC:

AN:

160710

AF XY:

0.000129

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000802

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000852

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000968

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000967

AC:

AN:

1024290

Hom.:

Cov.:

AF XY:

0.000115

AC XY:

AN XY:

521144

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24196

American (AMR)

AF:

0.0000850

AC:

AN:

35292

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22824

East Asian (EAS)

AF:

0.0000580

AC:

AN:

34494

South Asian (SAS)

AF:

0.000473

AC:

AN:

71838

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49488

Middle Eastern (MID)

AF:

0.000200

AC:

AN:

4988

European-Non Finnish (NFE)

AF:

0.0000775

AC:

AN:

735602

Other (OTH)

AF:

0.0000439

AC:

AN:

45568

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000595

AC:

AN:

151270

Hom.:

Cov.:

AF XY:

0.000108

AC XY:

AN XY:

73852

show subpopulations

African (AFR)

AF:

0.0000485

AC:

AN:

41238

American (AMR)

AF:

0.00

AC:

AN:

15154

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3464

East Asian (EAS)

AF:

0.000196

AC:

AN:

5108

South Asian (SAS)

AF:

0.000626

AC:

AN:

4794

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10314

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0000442

AC:

AN:

67902

Other (OTH)

AF:

0.00

AC:

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000965

Hom.:

Bravo

AF:

0.0000491

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Hereditary cancer-predisposing syndrome

Uncertain:1Benign:1

May 25, 2017

Color Diagnostics, LLC DBA Color Health

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jan 20, 2025

Molecular Diagnostics Laboratory, Catalan Institute of Oncology

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

TP53 (NM_000546.5) c.993+313G>A is an intronic variant at or beyond +7/–21. In beta and gamma isoforms, the nomenclature of this variant is NM_0011216114.2 (beta isoform): c.*85G>A and NM_001126113.2 (gamma isoform): c.1038G>A; (p.Ser346=).This variant is found in 17/185965 alleles at a frequency of 0.009% in the gnomAD v2.1.1 database, non-cancer dataset. The SpliceAI algorithm predicts no significant impact on splicing on isoform NM_000546.5: c.993+313G>A, but can not predict the effect on isoform NM_0011216114.2 c.*85G>A. To our knowledge, neither relevant clinical data nor functional studies have been reported for this variant. This variant has been reported in ClinVar (3x likely benign) and LOVD (1x uncertain significance) databases. Based on currently available information, the variant c.993+313G>A should be considered an uncertain significance variant. -

Li-Fraumeni syndrome 1

Benign:1

Jul 07, 2023

KCCC/NGS Laboratory, Kuwait Cancer Control Center

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

TP53-related disorder

Benign:1

Dec 04, 2023

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

7.0

(source)

DANN

Benign

0.94

PhyloP100

-1.3

PromoterAI

-0.021

Neutral

(source)

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over