chr1-92509038-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001350197.2(EVI5):c.*4618C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,210 control chromosomes in the GnomAD database, including 55,693 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 0.85 ( 55691 hom., cov: 32)
Exomes 𝑓: 0.57 ( 2 hom. )
Consequence
EVI5
NM_001350197.2 3_prime_UTR
NM_001350197.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.609
Genes affected
EVI5 (HGNC:3501): (ecotropic viral integration site 5) Enables GTPase activator activity and small GTPase binding activity. Involved in positive regulation of GTPase activity and retrograde transport, endosome to Golgi. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVI5 | NM_001350197.2 | c.*4618C>T | 3_prime_UTR_variant | 20/20 | ENST00000684568.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVI5 | ENST00000684568.2 | c.*4618C>T | 3_prime_UTR_variant | 20/20 | NM_001350197.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.852 AC: 129625AN: 152078Hom.: 55632 Cov.: 32
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GnomAD4 exome AF: 0.571 AC: 8AN: 14Hom.: 2 Cov.: 0 AF XY: 0.600 AC XY: 6AN XY: 10
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GnomAD4 genome ? AF: 0.852 AC: 129746AN: 152196Hom.: 55691 Cov.: 32 AF XY: 0.855 AC XY: 63620AN XY: 74416
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32
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at