rs210798

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001130173.2(MYB):​c.763-418T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,006 control chromosomes in the GnomAD database, including 27,264 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 0.59 ( 27264 hom., cov: 33)

Consequence

MYB
NM_001130173.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.914
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MYBNM_001130173.2 linkuse as main transcriptc.763-418T>G intron_variant 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.763-418T>G intron_variant 1 NM_001130173.2 ENSP00000339992.5 P10242-4

Frequencies

GnomAD3 genomes
AF:
0.587
AC:
89212
AN:
151888
Hom.:
27232
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.780
Gnomad AMI
AF:
0.374
Gnomad AMR
AF:
0.553
Gnomad ASJ
AF:
0.467
Gnomad EAS
AF:
0.500
Gnomad SAS
AF:
0.554
Gnomad FIN
AF:
0.505
Gnomad MID
AF:
0.453
Gnomad NFE
AF:
0.510
Gnomad OTH
AF:
0.575
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.588
AC:
89304
AN:
152006
Hom.:
27264
Cov.:
33
AF XY:
0.585
AC XY:
43442
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.780
Gnomad4 AMR
AF:
0.553
Gnomad4 ASJ
AF:
0.467
Gnomad4 EAS
AF:
0.499
Gnomad4 SAS
AF:
0.554
Gnomad4 FIN
AF:
0.505
Gnomad4 NFE
AF:
0.510
Gnomad4 OTH
AF:
0.576
Alfa
AF:
0.552
Hom.:
6791
Bravo
AF:
0.599
Asia WGS
AF:
0.575
AC:
1974
AN:
3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
2.9
DANN
Benign
0.88

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: rs210798; hg19: chr6-135514558; API