X-74739454-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001008537.3(NEXMIF):c.4502T>A(p.Val1501Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000919 in 1,088,720 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001008537.3 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 |
---|---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.4502T>A | p.Val1501Asp | missense_variant | 4/4 | ENST00000055682.12 | NP_001008537.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.4502T>A | p.Val1501Asp | missense_variant | 4/4 | 1 | NM_001008537.3 | ENSP00000055682 | P1 | |
NEXMIF | ENST00000616200.2 | c.4502T>A | p.Val1501Asp | missense_variant | 4/5 | 1 | ENSP00000480284 | P1 | ||
NEXMIF | ENST00000642681.2 | c.*642T>A | 3_prime_UTR_variant | 3/3 | ENSP00000495800 |
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD4 exome AF: 9.19e-7 AC: 1AN: 1088720Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 355796
GnomAD4 genome Cov.: 21
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 10, 2023 | This sequence change replaces valine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 1501 of the NEXMIF protein (p.Val1501Asp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NEXMIF-related conditions. ClinVar contains an entry for this variant (Variation ID: 1000544). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Not Available". The aspartic acid amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at