17-31318616-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014210.4(EVI2A):āc.398T>Cā(p.Met133Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,613,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014210.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EVI2A | NM_014210.4 | c.398T>C | p.Met133Thr | missense_variant | 2/2 | ENST00000462804.3 | |
NF1 | NM_001042492.3 | c.4836-7204A>G | intron_variant | ENST00000358273.9 | |||
EVI2A | NM_001003927.3 | c.467T>C | p.Met156Thr | missense_variant | 3/3 | ||
NF1 | NM_000267.3 | c.4773-7204A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EVI2A | ENST00000462804.3 | c.398T>C | p.Met133Thr | missense_variant | 2/2 | 1 | NM_014210.4 | P2 | |
NF1 | ENST00000358273.9 | c.4836-7204A>G | intron_variant | 1 | NM_001042492.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250800Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135618
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461728Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727168
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.467T>C (p.M156T) alteration is located in exon 3 (coding exon 2) of the EVI2A gene. This alteration results from a T to C substitution at nucleotide position 467, causing the methionine (M) at amino acid position 156 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at