rs2294163

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001754.5(RUNX1):​c.58+13749C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,194 control chromosomes in the GnomAD database, including 2,657 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 0.17 ( 2657 hom., cov: 32)

Consequence

RUNX1
NM_001754.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0710
Variant links:
Genes affected
RUNX1 (HGNC:10471): (RUNX family transcription factor 1) Core binding factor (CBF) is a heterodimeric transcription factor that binds to the core element of many enhancers and promoters. The protein encoded by this gene represents the alpha subunit of CBF and is thought to be involved in the development of normal hematopoiesis. Chromosomal translocations involving this gene are well-documented and have been associated with several types of leukemia. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RUNX1NM_001754.5 linkuse as main transcriptc.58+13749C>T intron_variant ENST00000675419.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RUNX1ENST00000675419.1 linkuse as main transcriptc.58+13749C>T intron_variant NM_001754.5 A1Q01196-8

Frequencies

GnomAD3 genomes
AF:
0.168
AC:
25540
AN:
152076
Hom.:
2659
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0420
Gnomad AMI
AF:
0.156
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.219
Gnomad EAS
AF:
0.369
Gnomad SAS
AF:
0.290
Gnomad FIN
AF:
0.241
Gnomad MID
AF:
0.146
Gnomad NFE
AF:
0.197
Gnomad OTH
AF:
0.179
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.168
AC:
25538
AN:
152194
Hom.:
2657
Cov.:
32
AF XY:
0.175
AC XY:
13024
AN XY:
74398
show subpopulations
Gnomad4 AFR
AF:
0.0419
Gnomad4 AMR
AF:
0.210
Gnomad4 ASJ
AF:
0.219
Gnomad4 EAS
AF:
0.369
Gnomad4 SAS
AF:
0.290
Gnomad4 FIN
AF:
0.241
Gnomad4 NFE
AF:
0.197
Gnomad4 OTH
AF:
0.178
Alfa
AF:
0.199
Hom.:
4115
Bravo
AF:
0.160
Asia WGS
AF:
0.274
AC:
952
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.3
DANN
Benign
0.77

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2294163; hg19: chr21-36407390; API