rs1022775047
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001008537.3(NEXMIF):āc.2147T>Gā(p.Val716Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000496 in 1,209,661 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 (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V716M) has been classified as Uncertain significance.
Frequency
Consequence
NM_001008537.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEXMIF | NM_001008537.3 | c.2147T>G | p.Val716Gly | missense_variant | 3/4 | ENST00000055682.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEXMIF | ENST00000055682.12 | c.2147T>G | p.Val716Gly | missense_variant | 3/4 | 1 | NM_001008537.3 | P1 | |
NEXMIF | ENST00000616200.2 | c.2147T>G | p.Val716Gly | missense_variant | 3/5 | 1 | P1 | ||
NEXMIF | ENST00000642681.2 | c.2147T>G | p.Val716Gly | missense_variant | 3/3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000269 AC: 3AN: 111730Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33898
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097931Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363309
GnomAD4 genome ? AF: 0.0000269 AC: 3AN: 111730Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33898
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 01, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Dec 21, 2020 | Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at