rs1883067

Variant summary

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

The NM_001754.5(RUNX1):​c.58+20963A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0533 in 152,338 control chromosomes in the GnomAD database, including 302 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 0.053 ( 302 hom., cov: 32)

Consequence

RUNX1
NM_001754.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.993
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]

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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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0684 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RUNX1NM_001754.5 linkuse as main transcriptc.58+20963A>G intron_variant ENST00000675419.1 NP_001745.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RUNX1ENST00000675419.1 linkuse as main transcriptc.58+20963A>G intron_variant NM_001754.5 ENSP00000501943 A1Q01196-8

Frequencies

GnomAD3 genomes
AF:
0.0533
AC:
8108
AN:
152220
Hom.:
301
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0136
Gnomad AMI
AF:
0.0384
Gnomad AMR
AF:
0.0647
Gnomad ASJ
AF:
0.0524
Gnomad EAS
AF:
0.00346
Gnomad SAS
AF:
0.0300
Gnomad FIN
AF:
0.123
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.0701
Gnomad OTH
AF:
0.0440
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0532
AC:
8112
AN:
152338
Hom.:
302
Cov.:
32
AF XY:
0.0546
AC XY:
4069
AN XY:
74498
show subpopulations
Gnomad4 AFR
AF:
0.0136
Gnomad4 AMR
AF:
0.0646
Gnomad4 ASJ
AF:
0.0524
Gnomad4 EAS
AF:
0.00367
Gnomad4 SAS
AF:
0.0302
Gnomad4 FIN
AF:
0.123
Gnomad4 NFE
AF:
0.0701
Gnomad4 OTH
AF:
0.0435
Alfa
AF:
0.0638
Hom.:
461
Bravo
AF:
0.0484
Asia WGS
AF:
0.0150
AC:
54
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.41
DANN
Benign
0.36

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: rs1883067; hg19: chr21-36400176; API