rs210798

Positions:

• chr6-135193420-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914

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 (HGNC:):

ACMG classification

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
MYB	NM_001130173.2	c.763-418T>G		intron_variant		ENST00000341911.10	NP_001123645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYB	ENST00000341911.10	c.763-418T>G		intron_variant		1	NM_001130173.2	ENSP00000339992.5

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89212 AN: 151888 Hom.: 27232 Cov.: 33

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

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

Other links and lift over

dbSNP: rs210798; hg19: chr6-135514558;