17-31318858-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_014210.4(EVI2A):c.156C>T(p.Gly52=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000536 in 1,613,994 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00029 ( 5 hom. )
Consequence
EVI2A
NM_014210.4 synonymous
NM_014210.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.918
Genes affected
EVI2A (HGNC:3499): (ecotropic viral integration site 2A) Predicted to be integral component of 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 Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 17-31318858-G-A is Benign according to our data. Variant chr17-31318858-G-A is described in ClinVar as [Benign]. Clinvar id is 3044725.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.918 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVI2A | NM_014210.4 | c.156C>T | p.Gly52= | synonymous_variant | 2/2 | ENST00000462804.3 | |
NF1 | NM_001042492.3 | c.4836-6962G>A | intron_variant | ENST00000358273.9 | |||
EVI2A | NM_001003927.3 | c.225C>T | p.Gly75= | synonymous_variant | 3/3 | ||
NF1 | NM_000267.3 | c.4773-6962G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVI2A | ENST00000462804.3 | c.156C>T | p.Gly52= | synonymous_variant | 2/2 | 1 | NM_014210.4 | P2 | |
NF1 | ENST00000358273.9 | c.4836-6962G>A | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00288 AC: 438AN: 152110Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.000653 AC: 164AN: 251250Hom.: 4 AF XY: 0.000493 AC XY: 67AN XY: 135790
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GnomAD4 exome AF: 0.000292 AC: 427AN: 1461766Hom.: 5 Cov.: 31 AF XY: 0.000270 AC XY: 196AN XY: 727190
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GnomAD4 genome AF: 0.00288 AC: 438AN: 152228Hom.: 3 Cov.: 32 AF XY: 0.00285 AC XY: 212AN XY: 74438
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
EVI2A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 06, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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