rs78919815
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000038.6(APC):c.423-16A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00782 in 412,922 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000038.6 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: 0.00112 AC: 156AN: 138912Hom.: 1 Cov.: 32
GnomAD4 exome AF: 0.0112 AC: 3074AN: 273962Hom.: 4 Cov.: 0 AF XY: 0.0113 AC XY: 1547AN XY: 137076
GnomAD4 genome AF: 0.00112 AC: 156AN: 138960Hom.: 1 Cov.: 32 AF XY: 0.00120 AC XY: 81AN XY: 67504
ClinVar
Submissions by phenotype
not specified Benign:3
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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. -
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Familial adenomatous polyposis 1 Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
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APC-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Familial colorectal cancer Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at