chr6-135214883-C-T

Position:

• chr6-135214883-C-T

Variant summary

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

The NM_001130173.2(MYB):​c.2170-2981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,136 control chromosomes in the GnomAD database, including 2,609 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 0.16 (2609 hom., cov: 33)
• Consequence: MYB NM_001130173.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818

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]

LOC105378011 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MYB	NM_001130173.2	c.2170-2981C>T		intron_variant		ENST00000341911.10	NP_001123645.1
LOC105378011	XR_001744368.2	n.278+516G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MYB	ENST00000341911.10	c.2170-2981C>T		intron_variant		1	NM_001130173.2	ENSP00000339992	A1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25047 AN: 152018 Hom.: 2607 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.146

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.165 AC: 25082 AN: 152136 Hom.: 2609 Cov.: 33 AF XY: 0.162 AC XY: 12017 AN XY: 74386

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0904

Gnomad4 EAS AF: 0.0979

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0921

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.144

Alfa AF: 0.151 Hom.: 321

Bravo AF: 0.172

Asia WGS AF: 0.133 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.59

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: rs6936293; hg19: chr6-135536021;