chr21-34788691-T-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP2BS1

This summary comes from the ClinGen Evidence Repository: NM_001754.5(RUNX1):c.*3444A>G is an intronic variant. MAF of 0.001 (0.1%, 18/15,276 alleles) in the Latino/Admixed American subpopulation of the gnomAD v3.1.2 cohort is ≥ 0.00015 (0.015%) (BS1). This variant is reported in 4 homozygotes in gnomAD v2.1.1 (BP2). 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: BS1 and BP2 LINK:https://erepo.genome.network/evrepo/ui/classification/CA10653547/MONDO:0011071/008

Frequency

Genomes: 𝑓 0.0021 ( 4 hom., cov: 32)
Exomes 𝑓: 0.00064 ( 0 hom. )

Consequence

RUNX1
NM_001754.5 3_prime_UTR

Scores

2

Clinical Significance

Likely benign reviewed by expert panel B:2

Conservation

PhyloP100: 0.885
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 Likely_benign. Variant got -5 ACMG points.

BP2
For more information check the summary or visit ClinGen Evidence Repository.
BS1
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.*3444A>G 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.*3444A>G 3_prime_UTR_variant 9/9 NM_001754.5 ENSP00000501943 A1Q01196-8
RUNX1ENST00000300305.7 linkuse as main transcriptc.*3444A>G 3_prime_UTR_variant 8/81 ENSP00000300305 A1Q01196-8
RUNX1ENST00000344691.8 linkuse as main transcriptc.*3444A>G 3_prime_UTR_variant 6/61 ENSP00000340690 P4Q01196-1
RUNX1ENST00000437180.5 linkuse as main transcriptc.*3444A>G 3_prime_UTR_variant 9/95 ENSP00000409227 A1Q01196-8

Frequencies

GnomAD3 genomes
AF:
0.00209
AC:
318
AN:
152174
Hom.:
4
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000338
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00118
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0223
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000617
Gnomad OTH
AF:
0.00192
GnomAD4 exome
AF:
0.000640
AC:
52
AN:
81190
Hom.:
0
Cov.:
0
AF XY:
0.000829
AC XY:
31
AN XY:
37376
show subpopulations
Gnomad4 AFR exome
AF:
0.000515
Gnomad4 AMR exome
AF:
0.00240
Gnomad4 ASJ exome
AF:
0.00176
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0227
Gnomad4 NFE exome
AF:
0.000240
Gnomad4 OTH exome
AF:
0.00177
GnomAD4 genome
AF:
0.00209
AC:
318
AN:
152292
Hom.:
4
Cov.:
32
AF XY:
0.00286
AC XY:
213
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.000337
Gnomad4 AMR
AF:
0.00118
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0223
Gnomad4 NFE
AF:
0.000617
Gnomad4 OTH
AF:
0.00190
Alfa
AF:
0.00138
Hom.:
0
Bravo
AF:
0.000790
Asia WGS
AF:
0.000289
AC:
1
AN:
3476

ClinVar

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

Submissions by phenotype

Hereditary thrombocytopenia and hematologic cancer predisposition syndrome Benign:1
Likely benign, reviewed by expert panelcurationClinGen Myeloid Malignancy Variant Curation Expert PanelJul 08, 2022NM_001754.5(RUNX1):c.*3444A>G is an intronic variant. MAF of 0.001 (0.1%, 18/15,276 alleles) in the Latino/Admixed American subpopulation of the gnomAD v3.1.2 cohort is ≥ 0.00015 (0.015%) (BS1). This variant is reported in 4 homozygotes in gnomAD v2.1.1 (BP2). 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: BS1 and BP2 -
Hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
3.7
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: rs183666715; hg19: chr21-36160988; API