rs73555746

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_001130173.2(MYB):ā€‹c.1886A>Cā€‹(p.Glu629Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000344 in 1,614,140 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: š‘“ 0.0019 ( 1 hom., cov: 32)
Exomes š‘“: 0.00018 ( 2 hom. )

Consequence

MYB
NM_001130173.2 missense

Scores

2
5
12

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 8.37
Variant links:
Genes affected
MYB (HGNC:7545): (MYB proto-oncogene, transcription factor) This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator. This protein plays an essential role in the regulation of hematopoiesis. This gene may be aberrently expressed or rearranged or undergo translocation in leukemias and lymphomas, and is considered to be an oncogene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0054531693).
BP6
Variant 6-135200351-A-C is Benign according to our data. Variant chr6-135200351-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 3035642.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 293 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYBNM_001130173.2 linkuse as main transcriptc.1886A>C p.Glu629Ala missense_variant 13/16 ENST00000341911.10 NP_001123645.1 P10242-4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MYBENST00000341911.10 linkuse as main transcriptc.1886A>C p.Glu629Ala missense_variant 13/161 NM_001130173.2 ENSP00000339992.5 P10242-4

Frequencies

GnomAD3 genomes
AF:
0.00191
AC:
290
AN:
152182
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00652
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000785
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.000506
AC:
127
AN:
250926
Hom.:
1
AF XY:
0.000324
AC XY:
44
AN XY:
135608
show subpopulations
Gnomad AFR exome
AF:
0.00708
Gnomad AMR exome
AF:
0.000260
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000177
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000179
AC:
262
AN:
1461840
Hom.:
2
Cov.:
31
AF XY:
0.000138
AC XY:
100
AN XY:
727212
show subpopulations
Gnomad4 AFR exome
AF:
0.00612
Gnomad4 AMR exome
AF:
0.000335
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000153
Gnomad4 OTH exome
AF:
0.000397
GnomAD4 genome
AF:
0.00192
AC:
293
AN:
152300
Hom.:
1
Cov.:
32
AF XY:
0.00189
AC XY:
141
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.00657
Gnomad4 AMR
AF:
0.000784
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.000449
Hom.:
0
Bravo
AF:
0.00229
ESP6500AA
AF:
0.00749
AC:
33
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000601
AC:
73
Asia WGS
AF:
0.000866
AC:
4
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

MYB-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 06, 2019This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.21
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.24
T;.;T;T;.;T;T;.;.;.;.;.
Eigen
Uncertain
0.68
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Pathogenic
0.97
D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
0.028
D
MetaRNN
Benign
0.0055
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.89
T
MutationAssessor
Benign
1.4
.;.;.;.;.;L;.;.;.;.;L;.
PrimateAI
Uncertain
0.66
T
PROVEAN
Uncertain
-2.6
.;D;.;D;N;N;N;D;D;D;D;N
REVEL
Benign
0.14
Sift
Benign
0.033
.;D;.;D;T;T;T;T;D;D;D;T
Sift4G
Benign
0.43
T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
1.0
D;D;.;.;D;P;.;.;.;.;.;.
Vest4
0.38
MVP
0.27
MPC
0.67
ClinPred
0.066
T
GERP RS
4.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.20
gMVP
0.48

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: rs73555746; hg19: chr6-135521489; COSMIC: COSV104413622; COSMIC: COSV104413622; API