dbSNP rs210796: MYB:c.306+87A>T (chr6-135189970-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001130173.2(MYB):c.306+87A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 1,469,238 control chromosomes in the GnomAD database, including 114,635 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.37 ( 10489 hom., cov: 33)

Exomes 𝑓: 0.40 ( 104146 hom. )

Consequence

MYB
NM_001130173.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.706

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:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130173.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYB	NM_001130173.2	MANE Select	c.306+87A>T	intron	N/A	NP_001123645.1	P10242-4
MYB	NM_001161656.2		c.306+87A>T	intron	N/A	NP_001155128.1	P10242-7
MYB	NM_001161658.2		c.306+87A>T	intron	N/A	NP_001155130.1	P10242-8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MYB	ENST00000341911.10	TSL:1 MANE Select	c.306+87A>T	intron	N/A	ENSP00000339992.5	P10242-4
MYB	ENST00000528774.5	TSL:1	c.306+87A>T	intron	N/A	ENSP00000434723.1	P10242-7
MYB	ENST00000534121.5	TSL:1	c.306+87A>T	intron	N/A	ENSP00000432851.1	P10242-8

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

56017

AN:

151988

Hom.:

10485

Cov.:

show subpopulations

Gnomad AFR

AF:

0.305

Gnomad AMI

AF:

0.317

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.370

Gnomad EAS

AF:

0.402

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.417

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.389

Gnomad OTH

AF:

0.371

GnomAD4 exome

AF:

0.397

AC:

522875

AN:

1317132

Hom.:

104146

Cov.:

AF XY:

0.396

AC XY:

260664

AN XY:

657878

show subpopulations

African (AFR)

AF:

0.294

AC:

8705

AN:

29646

American (AMR)

AF:

0.450

AC:

16956

AN:

37682

Ashkenazi Jewish (ASJ)

AF:

0.376

AC:

8825

AN:

23476

East Asian (EAS)

AF:

0.350

AC:

13543

AN:

38684

South Asian (SAS)

AF:

0.403

AC:

31296

AN:

77648

European-Finnish (FIN)

AF:

0.407

AC:

20957

AN:

51548

Middle Eastern (MID)

AF:

0.295

AC:

1573

AN:

5328

European-Non Finnish (NFE)

AF:

0.400

AC:

399277

AN:

998036

Other (OTH)

AF:

0.395

AC:

21743

AN:

55084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

15861

31721

47582

63442

79303

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12240

24480

36720

48960

61200

<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:

0.368

AC:

56039

AN:

152106

Hom.:

10489

Cov.:

AF XY:

0.371

AC XY:

27565

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.304

AC:

12630

AN:

41482

American (AMR)

AF:

0.405

AC:

6197

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.370

AC:

1284

AN:

3472

East Asian (EAS)

AF:

0.401

AC:

2079

AN:

5186

South Asian (SAS)

AF:

0.382

AC:

1843

AN:

4826

European-Finnish (FIN)

AF:

0.417

AC:

4402

AN:

10552

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.389

AC:

26431

AN:

67972

Other (OTH)

AF:

0.374

AC:

791

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1861

3722

5584

7445

9306

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

556

1112

1668

2224

2780

<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:

0.382

Hom.:

1405

Bravo

AF:

0.365

Asia WGS

AF:

0.410

AC:

1423

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

-0.71

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