X-74739427-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001008537.3(NEXMIF):c.4529G>A(p.Arg1510His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000503 in 1,193,689 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.4529G>A | p.Arg1510His | 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.4529G>A | p.Arg1510His | missense_variant | 4/4 | 1 | NM_001008537.3 | ENSP00000055682 | P1 | |
NEXMIF | ENST00000616200.2 | c.4529G>A | p.Arg1510His | missense_variant | 4/5 | 1 | ENSP00000480284 | P1 | ||
NEXMIF | ENST00000642681.2 | c.*669G>A | 3_prime_UTR_variant | 3/3 | ENSP00000495800 |
Frequencies
GnomAD3 genomes AF: 0.00000908 AC: 1AN: 110096Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32394
GnomAD3 exomes AF: 0.00000604 AC: 1AN: 165691Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 53303
GnomAD4 exome AF: 0.00000369 AC: 4AN: 1083541Hom.: 0 Cov.: 27 AF XY: 0.00000569 AC XY: 2AN XY: 351311
GnomAD4 genome AF: 0.0000182 AC: 2AN: 110148Hom.: 0 Cov.: 21 AF XY: 0.0000308 AC XY: 1AN XY: 32456
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 25, 2022 | 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The histidine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with NEXMIF-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 1510 of the NEXMIF protein (p.Arg1510His). - |
NEXMIF-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 17, 2023 | The NEXMIF c.4529G>A variant is predicted to result in the amino acid substitution p.Arg1510His. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0080% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/X-73959262-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at