rs113302588
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000546.6(TP53):c.783-33T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000127 in 1,587,600 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 (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_000546.6 intron
Scores
Clinical Significance
Conservation
Publications
- breast cancerInheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics
- Li-Fraumeni syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Orphanet
- Li-Fraumeni syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp
- adrenocortical carcinoma, hereditaryInheritance: AD Classification: STRONG Submitted by: Ambry Genetics
- sarcomaInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- bone marrow failure syndrome 5Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
- colorectal cancerInheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
- choroid plexus carcinomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000460 AC: 70AN: 152168Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.000155 AC: 31AN: 200158 AF XY: 0.0000933 show subpopulations
GnomAD4 exome AF: 0.0000906 AC: 130AN: 1435314Hom.: 0 Cov.: 33 AF XY: 0.0000745 AC XY: 53AN XY: 711778 show subpopulations
GnomAD4 genome AF: 0.000466 AC: 71AN: 152286Hom.: 0 Cov.: 31 AF XY: 0.000430 AC XY: 32AN XY: 74472 show subpopulations
ClinVar
Submissions by phenotype
Li-Fraumeni syndrome 1 Benign:2
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Hereditary cancer-predisposing syndrome Benign:2
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not specified Benign:1
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Hereditary breast ovarian cancer syndrome Benign:1
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Squamous cell carcinoma of the head and neck Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at