GeneBe

1-24963243-C-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000338888.4(RUNX3):​c.58+1271G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RUNX3
ENST00000338888.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.07

Publications

14 publications found
Variant links:
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]
RUNX3-AS1 (HGNC:40513): (RUNX3 antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RUNX3-AS1NR_183339.1 linkn.2562C>T non_coding_transcript_exon_variant Exon 6 of 6
RUNX3-AS1NR_183340.1 linkn.2334C>T non_coding_transcript_exon_variant Exon 4 of 4
RUNX3-AS1NR_183341.1 linkn.2102C>T non_coding_transcript_exon_variant Exon 4 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RUNX3ENST00000338888.4 linkc.58+1271G>A intron_variant Intron 2 of 6 1 ENSP00000343477.3 Q13761-2
RUNX3ENST00000479341.1 linkn.168+1271G>A intron_variant Intron 2 of 2 1
RUNX3ENST00000399916.5 linkc.58+1271G>A intron_variant Intron 1 of 5 2 ENSP00000382800.1 Q13761-2
RUNX3-AS1ENST00000456316.1 linkn.*146C>T downstream_gene_variant 5

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
336
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
238
African (AFR)
AF:
0.00
AC:
0
AN:
4
American (AMR)
AF:
0.00
AC:
0
AN:
6
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2
East Asian (EAS)
AF:
0.00
AC:
0
AN:
8
South Asian (SAS)
AF:
0.00
AC:
0
AN:
12
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
8
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
278
Other (OTH)
AF:
0.00
AC:
0
AN:
14
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
5.9
DANN
Benign
0.74
PhyloP100
-1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs72657048; hg19: chr1-25289734; API