chr2-151275564-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004688.3(NMI):c.554G>A(p.Arg185Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,614,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NMI | NM_004688.3 | c.554G>A | p.Arg185Gln | missense_variant | 6/8 | ENST00000243346.10 | NP_004679.2 | |
NMI | XM_047446270.1 | c.827G>A | p.Arg276Gln | missense_variant | 6/8 | XP_047302226.1 | ||
NMI | XM_005246941.3 | c.554G>A | p.Arg185Gln | missense_variant | 6/8 | XP_005246998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NMI | ENST00000243346.10 | c.554G>A | p.Arg185Gln | missense_variant | 6/8 | 1 | NM_004688.3 | ENSP00000243346 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000636 AC: 16AN: 251480Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135912
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727242
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2023 | The c.554G>A (p.R185Q) alteration is located in exon 6 (coding exon 5) of the NMI gene. This alteration results from a G to A substitution at nucleotide position 554, causing the arginine (R) at amino acid position 185 to be replaced by a glutamine (Q). 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