3-169362397-T-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004991.4(MECOM):c.375+18790A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 151,872 control chromosomes in the GnomAD database, including 949 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 ( 949 hom., cov: 32)
Consequence
MECOM
NM_004991.4 intron
NM_004991.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.960
Genes affected
MECOM (HGNC:3498): (MDS1 and EVI1 complex locus) The protein encoded by this gene is a transcriptional regulator and oncoprotein that may be involved in hematopoiesis, apoptosis, development, and cell differentiation and proliferation. The encoded protein can interact with CTBP1, SMAD3, CREBBP, KAT2B, MAPK8, and MAPK9. This gene can undergo translocation with the AML1 gene, resulting in overexpression of this gene and the onset of leukemia. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]
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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=-0.57).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MECOM | NM_004991.4 | c.375+18790A>C | intron_variant | ENST00000651503.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MECOM | ENST00000651503.2 | c.375+18790A>C | intron_variant | NM_004991.4 | P3 | ||||
MECOM | ENST00000485957.1 | n.621+18790A>C | intron_variant, non_coding_transcript_variant | 1 | |||||
MECOM | ENST00000494292.6 | c.375+18790A>C | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.100 AC: 15201AN: 151754Hom.: 946 Cov.: 32
GnomAD3 genomes
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15201
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.100 AC: 15232AN: 151872Hom.: 949 Cov.: 32 AF XY: 0.0985 AC XY: 7313AN XY: 74230
GnomAD4 genome
?
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15232
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151872
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32
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7313
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74230
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452
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at