rs17880172
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000546.6(TP53):c.782+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0003 in 1,560,724 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000546.6 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00167 AC: 254AN: 152002Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000430 AC: 108AN: 251242Hom.: 2 AF XY: 0.000287 AC XY: 39AN XY: 135794
GnomAD4 exome AF: 0.000152 AC: 214AN: 1408604Hom.: 1 Cov.: 29 AF XY: 0.000134 AC XY: 94AN XY: 703956
GnomAD4 genome AF: 0.00167 AC: 254AN: 152120Hom.: 1 Cov.: 31 AF XY: 0.00157 AC XY: 117AN XY: 74374
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:4
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This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Li-Fraumeni syndrome 1 Benign:2
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not specified Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Li-Fraumeni syndrome Benign:1
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Breast and/or ovarian cancer Benign:1
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Hereditary breast ovarian cancer syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at