6-135201679-CA-TG

Variant names:

• chr6-135201679-CA-TG
• NM_001130173.2:c.1991_1992delCAinsTG
• MYB p.Ser664Leu

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001130173.2(MYB):​c.1991_1992delCAinsTG​(p.Ser664Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MYB NM_001130173.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYB	NM_001130173.2	MANE Select	c.1991_1992delCAinsTG	p.Ser664Leu	missense	N/A	NP_001123645.1	P10242-4
	MYB	NM_001161656.2		c.1982_1983delCAinsTG	p.Ser661Leu	missense	N/A	NP_001155128.1	P10242-7
	MYB	NM_001161658.2		c.1943_1944delCAinsTG	p.Ser648Leu	missense	N/A	NP_001155130.1	P10242-8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYB	ENST00000341911.10	TSL:1 MANE Select	c.1991_1992delCAinsTG	p.Ser664Leu	missense	N/A	ENSP00000339992.5	P10242-4
	MYB	ENST00000528774.5	TSL:1	c.1982_1983delCAinsTG	p.Ser661Leu	missense	N/A	ENSP00000434723.1	P10242-7
	MYB	ENST00000534121.5	TSL:1	c.1943_1944delCAinsTG	p.Ser648Leu	missense	N/A	ENSP00000432851.1	P10242-8

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr6-135522817;