21-34924881-T-C

Position:

• chr21-34924881-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001754.5(RUNX1):​c.59-31918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,088 control chromosomes in the GnomAD database, including 48,511 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 0.78 (48511 hom., cov: 31)
• Consequence: RUNX1 NM_001754.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RUNX1	NM_001754.5	c.59-31918A>G		intron_variant		ENST00000675419.1	NP_001745.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RUNX1	ENST00000675419.1	c.59-31918A>G		intron_variant			NM_001754.5	ENSP00000501943	A1

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118559 AN: 151970 Hom.: 48488 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.791

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.780 AC: 118633 AN: 152088 Hom.: 48511 Cov.: 31 AF XY: 0.783 AC XY: 58210 AN XY: 74360

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.791

Alfa AF: 0.879 Hom.: 117718

Bravo AF: 0.762

Asia WGS AF: 0.874 AC: 3037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.21
DANN	Benign	0.61

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

Other links and lift over

dbSNP: rs4817699; hg19: chr21-36297178;