chr2-151270701-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004688.3(NMI):c.916G>A(p.Glu306Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000224 in 1,611,960 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004688.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NMI | NM_004688.3 | c.916G>A | p.Glu306Lys | missense_variant | 8/8 | ENST00000243346.10 | NP_004679.2 | |
NMI | XM_047446270.1 | c.1189G>A | p.Glu397Lys | missense_variant | 8/8 | XP_047302226.1 | ||
NMI | XM_005246941.3 | c.916G>A | p.Glu306Lys | missense_variant | 8/8 | XP_005246998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NMI | ENST00000243346.10 | c.916G>A | p.Glu306Lys | missense_variant | 8/8 | 1 | NM_004688.3 | ENSP00000243346 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000264 AC: 66AN: 250154Hom.: 0 AF XY: 0.000348 AC XY: 47AN XY: 135212
GnomAD4 exome AF: 0.000228 AC: 333AN: 1459656Hom.: 2 Cov.: 30 AF XY: 0.000249 AC XY: 181AN XY: 726144
GnomAD4 genome AF: 0.000184 AC: 28AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2023 | The c.916G>A (p.E306K) alteration is located in exon 8 (coding exon 7) of the NMI gene. This alteration results from a G to A substitution at nucleotide position 916, causing the glutamic acid (E) at amino acid position 306 to be replaced by a lysine (K). 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