rs12660713
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001130173.2(MYB):c.1204-103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,584,834 control chromosomes in the GnomAD database, including 9,927 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 0.10 ( 853 hom., cov: 32)
Exomes 𝑓: 0.11 ( 9074 hom. )
Consequence
MYB
NM_001130173.2 intron
NM_001130173.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.302
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=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYB | NM_001130173.2 | c.1204-103G>A | intron_variant | ENST00000341911.10 | NP_001123645.1 | |||
LOC105378011 | XR_001744368.2 | n.279-858C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYB | ENST00000341911.10 | c.1204-103G>A | intron_variant | 1 | NM_001130173.2 | ENSP00000339992 | A1 |
Frequencies
GnomAD3 genomes AF: 0.102 AC: 15551AN: 152052Hom.: 855 Cov.: 32
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GnomAD4 exome AF: 0.111 AC: 159031AN: 1432664Hom.: 9074 Cov.: 31 AF XY: 0.112 AC XY: 79378AN XY: 711452
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GnomAD4 genome AF: 0.102 AC: 15553AN: 152170Hom.: 853 Cov.: 32 AF XY: 0.101 AC XY: 7484AN XY: 74382
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at