rs13157
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004350.3(RUNX3):c.*936C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 151,806 control chromosomes in the GnomAD database, including 3,332 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 0.15 ( 3332 hom., cov: 30)
Exomes 𝑓: 0.037 ( 0 hom. )
Consequence
RUNX3
NM_004350.3 3_prime_UTR
NM_004350.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0700
Genes affected
RUNX3 (HGNC:10473): (RUNX family transcription factor 3) This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUNX3 | NM_004350.3 | c.*936C>T | 3_prime_UTR_variant | 5/5 | ENST00000308873.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUNX3 | ENST00000308873.11 | c.*936C>T | 3_prime_UTR_variant | 5/5 | 1 | NM_004350.3 | |||
RUNX3 | ENST00000338888.4 | c.*936C>T | 3_prime_UTR_variant | 7/7 | 1 | P1 | |||
RUNX3 | ENST00000399916.5 | c.*936C>T | 3_prime_UTR_variant | 6/6 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.148 AC: 22365AN: 151476Hom.: 3317 Cov.: 30
GnomAD3 genomes
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GnomAD4 exome AF: 0.0370 AC: 8AN: 216Hom.: 0 Cov.: 0 AF XY: 0.0441 AC XY: 6AN XY: 136
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GnomAD4 genome ? AF: 0.148 AC: 22415AN: 151590Hom.: 3332 Cov.: 30 AF XY: 0.146 AC XY: 10828AN XY: 74126
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at