21-34788158-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

This summary comes from the ClinGen Evidence Repository: The c.*3977G>A variant in the 3' UTR has an MAF of 0.003831 (0.38%, 12/3132 alleles) in the East Asian subpopulation of the gnomAD v3 cohort and is ≥ 0.0015 (0.15%) (BA1). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1. LINK:https://erepo.genome.network/evrepo/ui/classification/CA10650402/MONDO:0011071/008

Frequency

Genomes: 𝑓 0.00016 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00036 ( 0 hom. )

Consequence

RUNX1
NM_001754.5 3_prime_UTR

Scores

2

Clinical Significance

Benign reviewed by expert panel B:2

Conservation

PhyloP100: -1.43
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 -8 ACMG points.

BA1
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RUNX1NM_001754.5 linkuse as main transcriptc.*3977G>A 3_prime_UTR_variant 9/9 ENST00000675419.1 NP_001745.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RUNX1ENST00000675419.1 linkuse as main transcriptc.*3977G>A 3_prime_UTR_variant 9/9 NM_001754.5 ENSP00000501943 A1Q01196-8
RUNX1ENST00000300305.7 linkuse as main transcriptc.*3977G>A 3_prime_UTR_variant 8/81 ENSP00000300305 A1Q01196-8
RUNX1ENST00000344691.8 linkuse as main transcriptc.*3977G>A 3_prime_UTR_variant 6/61 ENSP00000340690 P4Q01196-1
RUNX1ENST00000437180.5 linkuse as main transcriptc.*3977G>A 3_prime_UTR_variant 9/95 ENSP00000409227 A1Q01196-8

Frequencies

GnomAD3 genomes
AF:
0.000164
AC:
25
AN:
152208
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00423
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000358
AC:
29
AN:
81110
Hom.:
0
Cov.:
0
AF XY:
0.000375
AC XY:
14
AN XY:
37310
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00219
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000200
Gnomad4 OTH exome
AF:
0.000443
GnomAD4 genome
AF:
0.000158
AC:
24
AN:
152326
Hom.:
0
Cov.:
32
AF XY:
0.000174
AC XY:
13
AN XY:
74500
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00405
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.000125
Asia WGS
AF:
0.00144
AC:
5
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Hereditary thrombocytopenia and hematologic cancer predisposition syndrome Benign:1
Benign, reviewed by expert panelcurationClinGen Myeloid Malignancy Variant Curation Expert PanelMay 13, 2020The c.*3977G>A variant in the 3' UTR has an MAF of 0.003831 (0.38%, 12/3132 alleles) in the East Asian subpopulation of the gnomAD v3 cohort and is >= 0.0015 (0.15%) (BA1). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1. -
Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Benign:1
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.57
DANN
Benign
0.67

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: rs189557277; hg19: chr21-36160455; API