17-31305016-GT-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_006495.4(EVI2B):c.593del(p.Asn198ThrfsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,920 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000034 ( 0 hom. )
Consequence
EVI2B
NM_006495.4 frameshift
NM_006495.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.440
Genes affected
EVI2B (HGNC:3500): (ecotropic viral integration site 2B) Involved in positive regulation of granulocyte differentiation. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
NF1 (HGNC:7765): (neurofibromin 1) This gene product appears to function as a negative regulator of the ras signal transduction pathway. Mutations in this gene have been linked to neurofibromatosis type 1, juvenile myelomonocytic leukemia and Watson syndrome. The mRNA for this gene is subject to RNA editing (CGA>UGA->Arg1306Term) resulting in premature translation termination. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVI2B | NM_006495.4 | c.593del | p.Asn198ThrfsTer6 | frameshift_variant | 2/2 | ENST00000330927.5 | |
NF1 | NM_001042492.3 | c.4836-20797del | intron_variant | ENST00000358273.9 | |||
NF1 | NM_000267.3 | c.4773-20797del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVI2B | ENST00000330927.5 | c.593del | p.Asn198ThrfsTer6 | frameshift_variant | 2/2 | 1 | NM_006495.4 | P1 | |
NF1 | ENST00000358273.9 | c.4836-20797del | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152060Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251148Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135728
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GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.0000371 AC XY: 27AN XY: 727236
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GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 152060Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74298
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at