rs199960807
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001008537.3(NEXMIF):c.133G>A(p.Ala45Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000759 in 1,205,848 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 259 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001008537.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.133G>A | p.Ala45Thr | missense_variant | 3/4 | ENST00000055682.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.133G>A | p.Ala45Thr | missense_variant | 3/4 | 1 | NM_001008537.3 | P1 | |
NEXMIF | ENST00000616200.2 | c.133G>A | p.Ala45Thr | missense_variant | 3/5 | 1 | P1 | ||
NEXMIF | ENST00000642681.2 | c.133G>A | p.Ala45Thr | missense_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.000315 AC: 35AN: 111220Hom.: 0 Cov.: 23 AF XY: 0.000239 AC XY: 8AN XY: 33408
GnomAD3 exomes AF: 0.000284 AC: 50AN: 176128Hom.: 0 AF XY: 0.000241 AC XY: 15AN XY: 62152
GnomAD4 exome AF: 0.000804 AC: 880AN: 1094574Hom.: 0 Cov.: 30 AF XY: 0.000697 AC XY: 251AN XY: 360152
GnomAD4 genome ? AF: 0.000315 AC: 35AN: 111274Hom.: 0 Cov.: 23 AF XY: 0.000239 AC XY: 8AN XY: 33472
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 30, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | NEXMIF: BP4, BS2 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 19, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not specified Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 15, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 09, 2017 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at