rs17884293
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_006495.4(EVI2B):c.1019C>G(p.Pro340Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000363 in 1,614,132 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006495.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVI2B | NM_006495.4 | c.1019C>G | p.Pro340Arg | missense_variant | 2/2 | ENST00000330927.5 | |
NF1 | NM_001042492.3 | c.4836-21229G>C | intron_variant | ENST00000358273.9 | |||
NF1 | NM_000267.3 | c.4773-21229G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVI2B | ENST00000330927.5 | c.1019C>G | p.Pro340Arg | missense_variant | 2/2 | 1 | NM_006495.4 | P1 | |
NF1 | ENST00000358273.9 | c.4836-21229G>C | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00195 AC: 297AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000534 AC: 134AN: 251164Hom.: 0 AF XY: 0.000435 AC XY: 59AN XY: 135726
GnomAD4 exome AF: 0.000198 AC: 289AN: 1461858Hom.: 2 Cov.: 32 AF XY: 0.000176 AC XY: 128AN XY: 727232
GnomAD4 genome ? AF: 0.00195 AC: 297AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.00199 AC XY: 148AN XY: 74462
ClinVar
Submissions by phenotype
Neurofibromatosis, type 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Mar 15, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 11, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at