rs779441513
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001008537.3(NEXMIF):c.2986A>G(p.Met996Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,209,804 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 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 Benign (★).
Frequency
Consequence
NM_001008537.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.2986A>G | p.Met996Val | missense_variant | 3/4 | ENST00000055682.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.2986A>G | p.Met996Val | missense_variant | 3/4 | 1 | NM_001008537.3 | P1 | |
NEXMIF | ENST00000616200.2 | c.2986A>G | p.Met996Val | missense_variant | 3/5 | 1 | P1 | ||
NEXMIF | ENST00000642681.2 | c.2986A>G | p.Met996Val | missense_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111643Hom.: 0 Cov.: 22 AF XY: 0.0000295 AC XY: 1AN XY: 33849
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183018Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67588
GnomAD4 exome AF: 0.0000109 AC: 12AN: 1098161Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 4AN XY: 363539
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111643Hom.: 0 Cov.: 22 AF XY: 0.0000295 AC XY: 1AN XY: 33849
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at