chr2-151275562-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004688.3(NMI):āc.556A>Gā(p.Asn186Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,614,164 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 Uncertain significance (ā ).
Frequency
Consequence
NM_004688.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NMI | NM_004688.3 | c.556A>G | p.Asn186Asp | missense_variant | 6/8 | ENST00000243346.10 | NP_004679.2 | |
NMI | XM_047446270.1 | c.829A>G | p.Asn277Asp | missense_variant | 6/8 | XP_047302226.1 | ||
NMI | XM_005246941.3 | c.556A>G | p.Asn186Asp | missense_variant | 6/8 | XP_005246998.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NMI | ENST00000243346.10 | c.556A>G | p.Asn186Asp | missense_variant | 6/8 | 1 | NM_004688.3 | ENSP00000243346 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251480Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135912
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727246
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.556A>G (p.N186D) alteration is located in exon 6 (coding exon 5) of the NMI gene. This alteration results from a A to G substitution at nucleotide position 556, causing the asparagine (N) at amino acid position 186 to be replaced by an aspartic acid (D). 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