17-31304931-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006495.4(EVI2B):c.679T>A(p.Cys227Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000601 in 1,614,144 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVI2B | NM_006495.4 | c.679T>A | p.Cys227Ser | missense_variant | 2/2 | ENST00000330927.5 | |
NF1 | NM_001042492.3 | c.4836-20889A>T | intron_variant | ENST00000358273.9 | |||
NF1 | NM_000267.3 | c.4773-20889A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVI2B | ENST00000330927.5 | c.679T>A | p.Cys227Ser | missense_variant | 2/2 | 1 | NM_006495.4 | P1 | |
NF1 | ENST00000358273.9 | c.4836-20889A>T | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000319 AC: 80AN: 251056Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135684
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461834Hom.: 0 Cov.: 32 AF XY: 0.0000481 AC XY: 35AN XY: 727210
GnomAD4 genome ? AF: 0.000171 AC: 26AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | NF1: BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at