Genetic Variant MYB:n.*84G>A (chr6-135196858-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000528140.5(MYB):n.*84G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,584,834 control chromosomes in the GnomAD database, including 9,927 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 0.10 ( 853 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9074 hom. )

Consequence

MYB
ENST00000528140.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.302

Publications

6 publications found

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]

MYB links:

LOC105378011 (HGNC:):

LOC105378011 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528140.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MYB	NM_001130173.2	MANE Select	c.1204-103G>A	intron	N/A	NP_001123645.1
MYB	NR_134961.2		n.1542G>A	non_coding_transcript_exon	Exon 10 of 16
MYB	NM_001161656.2		c.1195-103G>A	intron	N/A	NP_001155128.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MYB	ENST00000528140.5	TSL:1	n.*84G>A	non_coding_transcript_exon	Exon 10 of 16	ENSP00000432877.1
MYB	ENST00000529262.5	TSL:1	n.*84G>A	non_coding_transcript_exon	Exon 10 of 16	ENSP00000433844.1
MYB	ENST00000531737.5	TSL:1	n.*84G>A	non_coding_transcript_exon	Exon 10 of 16	ENSP00000432168.1

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15551

AN:

152052

Hom.:

855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0890

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.0879

Gnomad EAS

AF:

0.0964

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.0867

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.0938

GnomAD4 exome

AF:

0.111

AC:

159031

AN:

1432664

Hom.:

9074

Cov.:

AF XY:

0.112

AC XY:

79378

AN XY:

711452

show subpopulations

African (AFR)

AF:

0.0893

AC:

2932

AN:

32830

American (AMR)

AF:

0.100

AC:

4287

AN:

42764

Ashkenazi Jewish (ASJ)

AF:

0.0897

AC:

2279

AN:

25412

East Asian (EAS)

AF:

0.123

AC:

4861

AN:

39428

South Asian (SAS)

AF:

0.134

AC:

11266

AN:

84036

European-Finnish (FIN)

AF:

0.0886

AC:

3562

AN:

40210

Middle Eastern (MID)

AF:

0.0793

AC:

448

AN:

5646

European-Non Finnish (NFE)

AF:

0.112

AC:

123015

AN:

1102850

Other (OTH)

AF:

0.107

AC:

6381

AN:

59488

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

7115

14230

21344

28459

35574

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4526

9052

13578

18104

22630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.102

AC:

15553

AN:

152170

Hom.:

853

Cov.:

AF XY:

0.101

AC XY:

7484

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0889

AC:

3690

AN:

41528

American (AMR)

AF:

0.104

AC:

1588

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0879

AC:

305

AN:

3470

East Asian (EAS)

AF:

0.0966

AC:

500

AN:

5174

South Asian (SAS)

AF:

0.139

AC:

672

AN:

4822

European-Finnish (FIN)

AF:

0.0867

AC:

918

AN:

10592

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7605

AN:

67978

Other (OTH)

AF:

0.0928

AC:

196

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

704

1409

2113

2818

3522

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.109

Hom.:

323

Bravo

AF:

0.101

Asia WGS

AF:

0.118

AC:

412

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.0

(source)

DANN

Benign

0.68

PhyloP100

-0.30

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over